Tumor endothelial marker 5-alpha molecules and uses thereof

ABSTRACT

The present invention provides Tumor Endothelial Marker 5α (TEM5α) polypeptides and nucleic acid molecules encoding the same. The invention also provides selective binding agents, vectors, host cells, and methods for producing TEM5α polypeptides. The invention further provides pharmaceutical compositions and methods for the diagnosis, treatment, amelioration, or prevention of diseases, disorders, and conditions associated with TEM5α polypeptides.

This application is a divisional of U.S. application Ser. No. 12/728,363filed Mar. 22, 2010, which is divisional of U.S. application Ser. No.10/271,697, filed Oct. 15, 2002, now U.S. Pat. No. 7,771,965, whichclaims the benefit of priority from U.S. Provisional Patent ApplicationNo. 60/329,223, filed on Oct. 12, 2001, the disclosure of which areexplicitly incorporated by reference herein.

REFERENCE TO THE SEQUENCE LISTING

The present application is being filed along with a Sequence Listing inelectronic format. The Sequence Listing is provided as a file entitledA-796-US-DIV3_ST25.txt, created Mar. 27, 2012, which is 107 KB in size.The information in the electronic format of the Sequence Listing isincorporated herein by reference in its entirety

FIELD OF THE INVENTION

The present invention relates to Tumor Endothelial Marker 5α (TEM5α)polypeptides and nucleic acid molecules encoding the same. The inventionalso relates to selective binding agents, vectors, host cells, andmethods for producing TEM5α polypeptides. The invention further relatesto pharmaceutical compositions and methods for the diagnosis, treatment,amelioration, or prevention of diseases, disorders, and conditionsassociated with TEM5α polypeptides.

BACKGROUND OF THE INVENTION

Technical advances in the identification, cloning, expression, andmanipulation of nucleic acid molecules and the deciphering of the humangenome have greatly accelerated the discovery of novel therapeutics.Rapid nucleic acid sequencing techniques can now generate sequenceinformation at unprecedented rates and, coupled with computationalanalyses, allow the assembly of overlapping sequences into partial andentire genomes and the identification of polypeptide-encoding regions. Acomparison of a predicted amino acid sequence against a databasecompilation of known amino acid sequences allows one to determine theextent of homology to previously identified sequences and/or structurallandmarks. The cloning and expression of a polypeptide-encoding regionof a nucleic acid molecule provides a polypeptide product for structuraland functional analyses. The manipulation of nucleic acid molecules andencoded polypeptides may confer advantageous properties on a product foruse as a therapeutic.

In spite of the significant technical advances in genome research overthe past decade, the potential for the development of novel therapeuticsbased on the human genome is still largely unrealized. Many genesencoding potentially beneficial polypeptide therapeutics or thoseencoding polypeptides, which may act as “targets” for therapeuticmolecules, have still not been identified. Accordingly, it is an objectof the invention to identify novel polypeptides, and nucleic acidmolecules encoding the same, which have diagnostic or therapeuticbenefit.

SUMMARY OF THE INVENTION

The present invention relates to novel TEM5α nucleic acid molecules andencoded polypeptides.

The invention provides for an isolated nucleic acid molecule comprisinga nucleotide sequence:

(a) as set forth in either SEQ ID NO: 1 or SEQ ID NO: 3;

(b) encoding the polypeptide as set forth in either SEQ ID NO: 2 or SEQID NO: 4;

(c) that hybridizes under at least moderately stringent conditions tothe complement of the nucleotide sequence of either (a) or (b), whereinthe nucleic acid molecule encodes a polypeptide having an activity ofthe polypeptide set forth in either SEQ ID NO: 2 or SEQ ID NO: 4; or

(d) complementary to the nucleotide sequence of any of (a)-(c).

The invention also provides for an isolated nucleic acid moleculecomprising:

(a) a nucleotide sequence encoding a polypeptide that is at least about70 percent identical to the polypeptide as set forth in either SEQ IDNO: 2 or SEQ ID NO: 4, wherein the encoded polypeptide has an activityof the polypeptide set forth in either SEQ ID NO: 2 or SEQ ID NO: 4;

(b) a nucleotide sequence encoding an allelic variant or splice variantof the nucleotide sequence as set forth in either SEQ ID NO: 1 or SEQ IDNO: 3 or the nucleotide sequence of (a);

(c) a region of the nucleotide sequence of either SEQ ID NO: 1 or SEQ IDNO: 3 or the nucleotide sequence of either (a) or (b), encoding apolypeptide fragment of at least about 25 amino acid residues, whereinthe polypeptide fragment has an activity of the polypeptide as set forthin either SEQ ID NO: 2 or SEQ ID NO: 4, or is antigenic;

(d) a region of the nucleotide sequence of either SEQ ID NO: 1 or SEQ IDNO: 3 or the nucleotide sequence of any of (a)-(c) comprising a fragmentof at least about 16 nucleotides;

(e) a nucleotide sequence that hybridizes under at least moderatelystringent conditions to the complement of the nucleotide sequence of anyof (a)-(d), wherein the nucleic acid molecule encodes a polypeptidehaving an activity of the polypeptide set forth in either SEQ ID NO: 2or SEQ ID NO: 4; or

(f) a nucleotide sequence complementary to the nucleotide sequence ofany of (a)-(e).

The invention further provides for an isolated nucleic acid moleculecomprising a nucleotide sequence:

(a) encoding a polypeptide as set forth in either SEQ ID NO: 2 or SEQ IDNO: 4 with at least one conservative amino acid substitution, whereinthe encoded polypeptide has an activity of the polypeptide set forth ineither SEQ ID NO: 2 or SEQ ID NO: 4;

(b) encoding a polypeptide as set forth in either SEQ ID NO: 2 or SEQ IDNO: 4 with at least one amino acid insertion, wherein the encodedpolypeptide has an activity of the polypeptide set forth in either SEQID NO: 2 or SEQ ID NO: 4;

(c) encoding a polypeptide as set forth in either SEQ ID NO: 2 or SEQ IDNO: 4 with at least one amino acid deletion, wherein the encodedpolypeptide has an activity of the polypeptide set forth in either SEQID NO: 2 or SEQ ID NO: 4;

(d) encoding a polypeptide as set forth in either SEQ ID NO: 2 or SEQ IDNO: 4 that has a C- and/or N-terminal truncation, wherein the encodedpolypeptide has an activity of the polypeptide set forth in either SEQID NO: 2 or SEQ ID NO: 4;

(e) encoding a polypeptide as set forth in either SEQ ID NO: 2 or SEQ IDNO: 4 with at least one modification that is an amino acid substitution,amino acid insertion, amino acid deletion, C-terminal truncation, orN-terminal truncation, wherein the encoded polypeptide has an activityof the polypeptide set forth in either SEQ ID NO: 2 or SEQ ID NO: 4;

(f) of any of (a)-(e) comprising a fragment of at least about 16nucleotides;

(g) that hybridizes under at least moderately stringent conditions tothe complement of the nucleotide sequence of any of (a)-(f), wherein thenucleic acid molecule encodes a polypeptide having an activity of thepolypeptide set forth in either SEQ ID NO: 2 or SEQ ID NO: 4; or

(h) complementary to the nucleotide sequence of any of (a)-(g).

The present invention provides for an isolated polypeptide comprisingthe amino acid sequence set forth in either SEQ ID NO: 2 or SEQ ID NO:4.

The invention also provides for an isolated polypeptide comprising:

(a) an amino acid sequence for an ortholog of either SEQ ID NO: 2 or SEQID NO: 4;

(b) an amino acid sequence that is at least about 70 percent identicalto the amino acid sequence of either SEQ ID NO: 2 or SEQ ID NO: 4,wherein the polypeptide has an activity of the polypeptide set forth ineither SEQ ID NO: 2 or SEQ ID NO: 4;

(c) a fragment of the amino acid sequence set forth in either SEQ ID NO:2 or SEQ ID NO: 4 comprising at least about 25 amino acid residues,wherein the fragment has an activity of the polypeptide set forth ineither SEQ ID NO: 2 or SEQ ID NO: 4, or is antigenic; or

(d) an amino acid sequence for an allelic variant or splice variant ofthe amino acid sequence as set forth in either SEQ ID NO: 2 or SEQ IDNO: 4, or the amino acid sequence of either (a) or (b).

The invention further provides for an isolated polypeptide comprising anamino acid sequence as set forth in either SEQ ID NO: 2 or SEQ ID NO: 4:

(a) with at least one conservative amino acid substitution;

(b) with at least one amino acid insertion;

(c) with at least one amino acid deletion;

(d) that has a C- and/or N-terminal truncation; or

(e) with at least one modification that is an amino acid substitution,amino acid insertion, amino acid deletion, C-terminal truncation, orN-terminal truncation;

wherein the polypeptide has an activity of the polypeptide set forth ineither SEQ ID NO: 2 or SEQ ID NO: 4.

Also provided are fusion polypeptides comprising TEM5α amino acidsequences.

The present invention also provides for an expression vector comprisingthe isolated nucleic acid molecules as set forth herein, recombinanthost cells comprising the recombinant nucleic acid molecules as setforth herein, and a method of producing a TEM5α polypeptide comprisingculturing the host cells and optionally isolating the polypeptide soproduced.

A transgenic non-human animal comprising a nucleic acid moleculeencoding a TEM5α polypeptide is also encompassed by the invention. TheTEM5α nucleic acid molecules are introduced into the animal in a mannerthat allows expression and increased levels of a TEM5α polypeptide,which may include increased circulating levels. Alternatively, the TEM5αnucleic acid molecules are introduced into the animal in a manner thatprevents expression of endogenous TEM5α polypeptide (i.e., generates atransgenic animal possessing a TEM5α polypeptide gene knockout). Thetransgenic non-human animal is preferably a mammal, and more preferablya rodent, such as a rat or a mouse.

Also provided are derivatives of the TEM5α polypeptides of the presentinvention.

Additionally provided are selective binding agents such as antibodiesand peptides capable of specifically binding the TEM5α polypeptides ofthe invention. Such antibodies and peptides may be agonistic orantagonistic.

Pharmaceutical compositions comprising the nucleotides, polypeptides, orselective binding agents of the invention and one or morepharmaceutically acceptable formulation agents are also encompassed bythe invention. The pharmaceutical compositions are used to providetherapeutically effective amounts of the nucleotides or polypeptides ofthe present invention. The invention is also directed to methods ofusing the polypeptides, nucleic acid molecules, and selective bindingagents.

The TEM5α polypeptides and nucleic acid molecules of the presentinvention may be used to treat, prevent, ameliorate, and/or detectdiseases and disorders, including those recited herein.

The present invention also provides a method of assaying test moleculesto identify a test molecule that binds to a TEM5α polypeptide. Themethod comprises contacting a TEM5α polypeptide with a test molecule todetermine the extent of binding of the test molecule to the polypeptide.The method further comprises determining whether such test molecules areagonists or antagonists of a TEM5α polypeptide. The present inventionfurther provides a method of testing the impact of molecules on theexpression of TEM5α polypeptide or on the activity of TEM5α polypeptide.

Methods of regulating expression and modulating (i.e., increasing ordecreasing) levels of a TEM5α polypeptide are also encompassed by theinvention. One method comprises administering to an animal a nucleicacid molecule encoding a TEM5α polypeptide. In another method, a nucleicacid molecule comprising elements that regulate or modulate theexpression of a TEM5α polypeptide may be administered. Examples of thesemethods include gene therapy, cell therapy, and anti-sense therapy asfurther described herein.

In another aspect of the present invention, TEM5α polypeptides can beused for identifying ligands thereof. Various forms of “expressioncloning” have been used for cloning ligands for receptors (See, e.g.,Davis et al., 1996, Cell, 87:1161-69). These and other TEM5α ligandcloning experiments are described in greater detail herein. Isolation ofthe TEM5α ligand(s) allows for the identification or development ofnovel agonists and/or antagonists of the TEM5α signaling pathway. Suchagonists and antagonists include TEM5α ligand(s), anti-TEM5α ligandantibodies and derivatives thereof, small molecules, or antisenseoligonucleotides, any of which can be used for potentially treating oneor more diseases or disorders, including those recited herein.

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A-1G show the nucleotide sequence of the human TEM5α gene (SEQ IDNO: 1) and the deduced amino acid sequence of human TEM5α polypeptide(SEQ ID NO: 2);

FIGS. 2A-2D show a nucleotide sequence (SEQ ID NO: 3) encoding solubleform of human TEM5α polypeptide (SEQ ID NO: 4);

FIGS. 3A-3B show an amino acid sequence alignment of human TEM5polypeptide (upper sequence; SEQ ID NO: 5) and human TEM5α polypeptide(lower sequence; SEQ ID NO: 2);

FIGS. 4A-4B illustrate the locations of several conserved domainspossessed by the human TEM5α polypeptide (SEQ ID NO: 2; FIG. 4A) and thesoluble form of the human TEM5α polypeptide (SEQ ID NO: 4; FIG. 4B), asindicated following a BLAST analysis of the amino acid sequences againstthe Conserved Domain Database.

DETAILED DESCRIPTION OF THE INVENTION

The section headings used herein are for organizational purposes onlyand are not to be construed as limiting the subject matter described.All references cited in this application are expressly incorporated byreference herein.

DEFINITIONS

The terms “TEM5α gene” or “TEM5α nucleic acid molecule” or “TEM5αpolynucleotide” refer to a nucleic acid molecule comprising orconsisting of a nucleotide sequence as set forth in either SEQ ID NO: 1or SEQ ID NO: 3, a nucleotide sequence encoding the polypeptide as setforth in either SEQ ID NO: 2 or SEQ ID NO: 4, and nucleic acid moleculesas defined herein.

The term “TEM5α polypeptide allelic variant” refers to one of severalpossible naturally occurring alternate forms of a gene occupying a givenlocus on a chromosome of an organism or a population of organisms.

The term “TEM5α polypeptide splice variant” refers to a nucleic acidmolecule, usually RNA, which is generated by alternative processing ofintron sequences in an RNA transcript of TEM5α polypeptide amino acidsequence as set forth in either SEQ ID NO: 2 or SEQ ID NO: 4.

The term “isolated nucleic acid molecule” refers to a nucleic acidmolecule of the invention that (1) has been separated from at leastabout 50 percent of proteins, lipids, carbohydrates, or other materialswith which it is naturally found when total nucleic acid is isolatedfrom the source cells, (2) is not linked to all or a portion of apolynucleotide to which the “isolated nucleic acid molecule” is linkedin nature, (3) is operably linked to a polynucleotide which it is notlinked to in nature, or (4) does not occur in nature as part of a largerpolynucleotide sequence. Preferably, the isolated nucleic acid moleculeof the present invention is substantially free from any othercontaminating nucleic acid molecule(s) or other contaminants that arefound in its natural environment that would interfere with its use inpolypeptide production or its therapeutic, diagnostic, prophylactic orresearch use.

The term “nucleic acid sequence” or “nucleic acid molecule” refers to aDNA or RNA sequence. The term encompasses molecules formed from any ofthe known base analogs of DNA and RNA such as, but not limited to4-acetylcytosine, 8-hydroxy-N-6-methyladenosine, aziridinyl-cytosine,pseudoisocytosine, 5-(carboxyhydroxylmethyl)uracil, 5-fluorouracil,5-bromouracil, 5-carboxymethylaminomethyl-2-thiouracil,5-carboxy-methylaminomethyluracil, dihydrouracil, inosine,N6-iso-pentenyladenine, 1-methyladenine, 1-methylpseudouracil,1-methylguanine, 1-methylinosine, 2,2-dimethyl-guanine, 2-methyladenine,2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-methyladenine,7-methylguanine, 5-methylaminomethyluracil,5-methoxyamino-methyl-2-thiouracil, beta-D-mannosylqueosine,5′-methoxycarbonyl-methyluracil, 5-methoxyuracil,2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid methylester,uracil-5-oxyacetic acid, oxybutoxosine, pseudouracil, queosine,2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil,5-methyluracil, N-uracil-5-oxyacetic acid methylester,uracil-5-oxyacetic acid, pseudouracil, queosine, 2-thiocytosine, and2,6-diaminopurine.

The term “vector” is used to refer to any molecule (e.g., nucleic acid,plasmid, or virus) used to transfer coding information to a host cell.

The term “expression vector” refers to a vector that is suitable fortransformation of a host cell and contains nucleic acid sequences thatdirect and/or control the expression of inserted heterologous nucleicacid sequences. Expression includes, but is not limited to, processessuch as transcription, translation, and RNA splicing, if introns arepresent.

The term “operably linked” is used herein to refer to an arrangement offlanking sequences wherein the flanking sequences so described areconfigured or assembled so as to perform their usual function. Thus, aflanking sequence operably linked to a coding sequence may be capable ofeffecting the replication, transcription and/or translation of thecoding sequence. For example, a coding sequence is operably linked to apromoter when the promoter is capable of directing transcription of thatcoding sequence. A flanking sequence need not be contiguous with thecoding sequence, so long as it functions correctly. Thus, for example,intervening untranslated yet transcribed sequences can be presentbetween a promoter sequence and the coding sequence and the promotersequence can still be considered “operably linked” to the codingsequence.

The term “host cell” is used to refer to a cell which has beentransformed, or is capable of being transformed with a nucleic acidsequence and then of expressing a selected gene of interest. The termincludes the progeny of the parent cell, whether or not the progeny isidentical in morphology or in genetic make-up to the original parent, solong as the selected gene is present.

The term “TEM5α polypeptide” refers to a polypeptide comprising theamino acid sequence of either SEQ ID NO: 2 or SEQ ID NO: 4 and relatedpolypeptides. Related polypeptides include TEM5α polypeptide fragments,TEM5α polypeptide orthologs, TEM5α polypeptide variants, and TEM5αpolypeptide derivatives, which possess at least one activity of thepolypeptide as set forth in either SEQ ID NO: 2 or SEQ ID NO: 4. TEM5αpolypeptides may be mature polypeptides, as defined herein, and may ormay not have an amino-terminal methionine residue, depending on themethod by which they are prepared.

The term “TEM5α polypeptide fragment” refers to a polypeptide thatcomprises a truncation at the amino-terminus (with or without a leadersequence) and/or a truncation at the carboxyl-terminus of thepolypeptide as set forth in either SEQ ID NO: 2 or SEQ ID NO: 4. Theterm “TEM5α polypeptide fragment” also refers to amino-terminal and/orcarboxyl-terminal truncations of TEM5α polypeptide orthologs, TEM5αpolypeptide derivatives, or TEM5α polypeptide variants, or toamino-terminal and/or carboxyl-terminal truncations of the polypeptidesencoded by TEM5α polypeptide allelic variants or TEM5α polypeptidesplice variants. TEM5α polypeptide fragments may result from alternativeRNA splicing or from in vivo protease activity. Membrane-bound forms ofa TEM5α polypeptide are also contemplated by the present invention. Inpreferred embodiments, truncations and/or deletions comprise about 10amino acids, or about 20 amino acids, or about 50 amino acids, or about75 amino acids, or about 100 amino acids, or more than about 100 aminoacids. The polypeptide fragments so produced will comprise about 25contiguous amino acids, or about 50 amino acids, or about 75 aminoacids, or about 100 amino acids, or about 150 amino acids, or about 200amino acids, or more than about 200 amino acids. Such TEM5α polypeptidefragments may optionally comprise an amino-terminal methionine residue.It will be appreciated that such fragments can be used, for example, togenerate antibodies to TEM5α polypeptides.

The term “TEM5α polypeptide ortholog” refers to a polypeptide fromanother species that corresponds to TEM5α polypeptide amino acidsequence as set forth in either SEQ ID NO: 2 or SEQ ID NO: 4. Forexample, mouse and human TEM5α polypeptides are considered orthologs ofeach other.

The term “TEM5α polypeptide variants” refers to TEM5α polypeptidescomprising amino acid sequences having one or more amino acid sequencesubstitutions, deletions (such as internal deletions and/or TEM5αpolypeptide fragments), and/or additions (such as internal additionsand/or TEM5α fusion polypeptides) as compared to the TEM5α polypeptideamino acid sequence set forth in either SEQ ID NO: 2 or SEQ ID NO: 4(with or without a leader sequence). Variants may be naturally occurring(e.g., TEM5α polypeptide allelic variants, TEM5α polypeptide orthologs,and TEM5α polypeptide splice variants) or artificially constructed. SuchTEM5α polypeptide variants may be prepared from the correspondingnucleic acid molecules having a DNA sequence that varies accordinglyfrom the DNA sequence as set forth in either SEQ ID NO: 1 or SEQ ID NO:3. In preferred embodiments, the variants have from 1 to 3, or from 1 to5, or from 1 to 10, or from 1 to 15, or from 1 to 20, or from 1 to 25,or from 1 to 50, or from 1 to 75, or from 1 to 100, or more than 100amino acid substitutions, insertions, additions and/or deletions,wherein the substitutions may be conservative, or non-conservative, orany combination thereof.

The term “TEM5α polypeptide derivatives” refers to the polypeptide asset forth in either SEQ ID NO: 2 or SEQ ID NO: 4, TEM5α polypeptidefragments, TEM5α polypeptide orthologs, or TEM5α polypeptide variants,as defined herein, that have been chemically modified. The term “TEM5αpolypeptide derivatives” also refers to the polypeptides encoded byTEM5α polypeptide allelic variants or TEM5α polypeptide splice variants,as defined herein, that have been chemically modified.

The term “mature TEM5α polypeptide” refers to a TEM5α polypeptidelacking a leader sequence. A mature TEM5α polypeptide may also includeother modifications such as proteolytic processing of the amino-terminus(with or without a leader sequence) and/or the carboxyl-terminus,cleavage of a smaller polypeptide from a larger precursor, N-linkedand/or O-linked glycosylation, and the like.

The term “TEM5α fusion polypeptide” refers to a fusion of one or moreamino acids (such as a heterologous protein or peptide) at the amino- orcarboxyl-terminus of the polypeptide as set forth in either SEQ ID NO: 2or SEQ ID NO: 4, TEM5α polypeptide fragments, TEM5α polypeptideorthologs, TEM5α polypeptide variants, or TEM5α derivatives, as definedherein. The term “TEM5α fusion polypeptide” also refers to a fusion ofone or more amino acids at the amino- or carboxyl-terminus of thepolypeptide encoded by TEM5α polypeptide allelic variants or TEM5αpolypeptide splice variants, as defined herein.

The term “biologically active TEM5α polypeptides” refers to TEM5αpolypeptides having at least one activity characteristic of thepolypeptide comprising the amino acid sequence of either SEQ ID NO: 2 orSEQ ID NO: 4. In addition, a TEM5α polypeptide may be active as animmunogen; that is, the TEM5α polypeptide contains at least one epitopeto which antibodies may be raised.

The term “isolated polypeptide” refers to a polypeptide of the presentinvention that (1) has been separated from at least about 50 percent ofpolynucleotides, lipids, carbohydrates, or other materials with which itis naturally found when isolated from the source cell, (2) is not linked(by covalent or noncovalent interaction) to all or a portion of apolypeptide to which the “isolated polypeptide” is linked in nature, (3)is operably linked (by covalent or noncovalent interaction) to apolypeptide with which it is not linked in nature, or (4) does not occurin nature. Preferably, the isolated polypeptide is substantially freefrom any other contaminating polypeptides or other contaminants that arefound in its natural environment that would interfere with itstherapeutic, diagnostic, prophylactic or research use.

The term “identity,” as known in the art, refers to a relationshipbetween the sequences of two or more polypeptide molecules or two ormore nucleic acid molecules, as determined by comparing the sequences.In the art, “identity” also means the degree of sequence relatednessbetween nucleic acid molecules or polypeptides, as the case may be, asdetermined by the match between strings of two or more nucleotide or twoor more amino acid sequences. “Identity” measures the percent ofidentical matches between the smaller of two or more sequences with gapalignments (if any) addressed by a particular mathematical model orcomputer program (i.e., “algorithms”).

The term “similarity” is a related concept, but in contrast to“identity,” “similarity” refers to a measure of relatedness thatincludes both identical matches and conservative substitution matches.If two polypeptide sequences have, for example, 10/20 identical aminoacids, and the remainder are all non-conservative substitutions, thenthe percent identity and similarity would both be 50%. If in the sameexample, there are five more positions where there are conservativesubstitutions, then the percent identity remains 50%, but the percentsimilarity would be 75% (15/20). Therefore, in cases where there areconservative substitutions, the percent similarity between twopolypeptides will be higher than the percent identity between those twopolypeptides.

The term “naturally occurring” or “native” when used in connection withbiological materials such as nucleic acid molecules, polypeptides, hostcells, and the like, refers to materials which are found in nature andare not manipulated by man. Similarly, “non-naturally occurring” or“non-native” as used herein refers to a material that is not found innature or that has been structurally modified or synthesized by man.When used in connection with nucleotides, the terms “naturallyoccurring” or “native” refer to the bases adenine (A), cytosine (C),guanine (G), thymine (T), and uracil (U). When used in connection withamino acids, the terms “naturally occurring” and “native” refer to the20 amino acids alanine (A), cysteine (C), aspartic acid (D), glutamicacid (E), phenylalanine (F), glycine (G), histidine (H), isoleucine (I),lysine (K), leucine (L), methionine (M), asparagine (N), proline (P),glutamine (Q), arginine (R), serine (S), threonine (T), valine (V),tryptophan (W), and tyrosine (Y).

The terms “effective amount” and “therapeutically effective amount” eachrefer to the amount of a TEM5α polypeptide or TEM5α nucleic acidmolecule used to support an observable level of one or more biologicalactivities of the TEM5α polypeptides as set forth herein.

The term “pharmaceutically acceptable carrier” or “physiologicallyacceptable carrier” as used herein refers to one or more formulationmaterials suitable for accomplishing or enhancing the delivery of theTEM5α polypeptide, TEM5α nucleic acid molecule, or TEM5α selectivebinding agent as a pharmaceutical composition.

The term “antigen” refers to a molecule or a portion of a moleculecapable of being bound by a selective binding agent, such as anantibody, and additionally capable of being used in an animal to produceantibodies capable of binding to an epitope of that antigen. An antigenmay have one or more epitopes.

The term “selective binding agent” refers to a molecule or moleculeshaving specificity for a TEM5α polypeptide. As used herein, the terms,“specific” and “specificity” refer to the ability of the selectivebinding agents to bind to human TEM5α polypeptides and not to bind tohuman non-TEM5α polypeptides. It will be appreciated, however, that theselective binding agents may also bind orthologs of the polypeptide asset forth in either SEQ ID NO: 2 or SEQ ID NO: 4, that is, interspeciesversions thereof, such as mouse and rat TEM5α polypeptides.

The term “transduction” is used to refer to the transfer of genes fromone bacterium to another, usually by a phage. “Transduction” also refersto the acquisition and transfer of eukaryotic cellular sequences byretroviruses.

The term “transfection” is used to refer to the uptake of foreign orexogenous DNA by a cell, and a cell has been “transfected” when theexogenous DNA has been introduced inside the cell membrane. A number oftransfection techniques are well known in the art and are disclosedherein. See, e.g., Graham et al., 1973, Virology 52:456; Sambrook etal., Molecular Cloning, A Laboratory Manual (Cold Spring HarborLaboratories, 1989); Davis et al., Basic Methods in Molecular Biology(Elsevier, 1986); and Chu et al., 1981, Gene 13:197. Such techniques canbe used to introduce one or more exogenous DNA moieties into suitablehost cells.

The term “transformation” as used herein refers to a change in a cell'sgenetic characteristics, and a cell has been transformed when it hasbeen modified to contain a new DNA. For example, a cell is transformedwhere it is genetically modified from its native state. Followingtransfection or transduction, the transforming DNA may recombine withthat of the cell by physically integrating into a chromosome of thecell, may be maintained transiently as an episomal element without beingreplicated, or may replicate independently as a plasmid. A cell isconsidered to have been stably transformed when the DNA is replicatedwith the division of the cell.

Relatedness of Nucleic Acid Molecules and/or Polypeptides

It is understood that related nucleic acid molecules include allelic orsplice variants of the nucleic acid molecule of either SEQ ID NO: 1 orSEQ ID NO: 3, and include sequences which are complementary to any ofthe above nucleotide sequences. Related nucleic acid molecules alsoinclude a nucleotide sequence encoding a polypeptide comprising orconsisting essentially of a substitution, modification, addition and/ordeletion of one or more amino acid residues compared to the polypeptideas set forth in either SEQ ID NO: 2 or SEQ ID NO: 4. Such related TEM5αpolypeptides may comprise, for example, an addition and/or a deletion ofone or more N-linked or O-linked glycosylation sites or an additionand/or a deletion of one or more cysteine residues.

Related nucleic acid molecules also include fragments of TEM5α nucleicacid molecules which encode a polypeptide of at least about 25contiguous amino acids, or about 50 amino acids, or about 75 aminoacids, or about 100 amino acids, or about 150 amino acids, or about 200amino acids, or more than about 200 amino acid residues of the TEM5αpolypeptide of either SEQ ID NO: 2 or SEQ ID NO: 4.

In addition, related TEM5α nucleic acid molecules also include thosemolecules which comprise nucleotide sequences which hybridize undermoderately or highly stringent conditions as defined herein with thefully complementary sequence of the TEM5α nucleic acid molecule ofeither SEQ ID NO: 1 or SEQ ID NO: 3, or of a molecule encoding apolypeptide, which polypeptide comprises the amino acid sequence asshown in either SEQ ID NO: 2 or SEQ ID NO: 4, or of a nucleic acidfragment as defined herein, or of a nucleic acid fragment encoding apolypeptide as defined herein. Hybridization probes may be preparedusing the TEM5α sequences provided herein to screen cDNA, genomic orsynthetic DNA libraries for related sequences. Regions of the DNA and/oramino acid sequence of TEM5α polypeptide that exhibit significantidentity to known sequences are readily determined using sequencealignment algorithms as described herein and those regions may be usedto design probes for screening.

The term “highly stringent conditions” refers to those conditions thatare designed to permit hybridization of DNA strands whose sequences arehighly complementary, and to exclude hybridization of significantlymismatched DNAs. Hybridization stringency is principally determined bytemperature, ionic strength, and the concentration of denaturing agentssuch as formamide. Examples of “highly stringent conditions” forhybridization and washing are 0.015 M sodium chloride, 0.0015 M sodiumcitrate at 65-68° C. or 0.015 M sodium chloride, 0.0015 M sodiumcitrate, and 50% formamide at 42° C. See Sambrook, Fritsch & Maniatis,Molecular Cloning: A Laboratory Manual (2nd ed., Cold Spring HarborLaboratory, 1989); Anderson et al., Nucleic Acid Hybridisation: APractical Approach Ch. 4 (IRL Press Limited).

More stringent conditions (such as higher temperature, lower ionicstrength, higher formamide, or other denaturing agent) may also beused—however, the rate of hybridization will be affected. Other agentsmay be included in the hybridization and washing buffers for the purposeof reducing non-specific and/or background hybridization. Examples are0.1% bovine serum albumin, 0.1% polyvinyl-pyrrolidone, 0.1% sodiumpyrophosphate, 0.1% sodium dodecylsulfate, NaDodSO₄, (SDS), ficoll,Denhardt's solution, sonicated salmon sperm DNA (or anothernon-complementary DNA), and dextran sulfate, although other suitableagents can also be used. The concentration and types of these additivescan be changed without substantially affecting the stringency of thehybridization conditions. Hybridization experiments are usually carriedout at pH 6.8-7.4; however, at typical ionic strength conditions, therate of hybridization is nearly independent of pH. See Anderson et al.,Nucleic Acid Hybridisation: A Practical Approach Ch. 4 (IRL PressLimited).

Factors affecting the stability of DNA duplex include base composition,length, and degree of base pair mismatch. Hybridization conditions canbe adjusted by one skilled in the art in order to accommodate thesevariables and allow DNAs of different sequence relatedness to formhybrids. The melting temperature of a perfectly matched DNA duplex canbe estimated by the following equation:

T_(m)(° C.)=81.5+16.6(log [Na+])+0.41(% G+C)−600/N−0.72 (% formamide)

where N is the length of the duplex formed, [Na+] is the molarconcentration of the sodium ion in the hybridization or washingsolution, % G+C is the percentage of (guanine+cytosine) bases in thehybrid. For imperfectly matched hybrids, the melting temperature isreduced by approximately 1° C. for each 1% mismatch.

The term “moderately stringent conditions” refers to conditions underwhich a DNA duplex with a greater degree of base pair mismatching thancould occur under “highly stringent conditions” is able to form.Examples of typical “moderately stringent conditions” are 0.015 M sodiumchloride, 0.0015 M sodium citrate at 50-65° C. or 0.015 M sodiumchloride, 0.0015 M sodium citrate, and 20% formamide at 37-50° C. By wayof example, “moderately stringent conditions” of 50° C. in 0.015 Msodium ion will allow about a 21% mismatch.

It will be appreciated by those skilled in the art that there is noabsolute distinction between “highly stringent conditions” and“moderately stringent conditions.” For example, at 0.015 M sodium ion(no formamide), the melting temperature of perfectly matched long DNA isabout 71° C. With a wash at 65° C. (at the same ionic strength), thiswould allow for approximately a 6% mismatch. To capture more distantlyrelated sequences, one skilled in the art can simply lower thetemperature or raise the ionic strength.

A good estimate of the melting temperature in 1M NaCl* foroligonucleotide probes up to about 20 nt is given by:

Tm=2° C. per A-T base pair+4° C. per G-C base pair

*The sodium ion concentration in 6× salt sodium citrate (SSC) is 1M. SeeSuggs et al., Developmental Biology Using Purified Genes 683 (Brown andFox, eds., 1981).

High stringency washing conditions for oligonucleotides are usually at atemperature of 0-5° C. below the Tm of the oligonucleotide in 6×SSC,0.1% SDS.

In another embodiment, related nucleic acid molecules comprise orconsist of a nucleotide sequence that is at least about 70 percentidentical to the nucleotide sequence as shown in either SEQ ID NO: 1 orSEQ ID NO: 3. In preferred embodiments, the nucleotide sequences areabout 75 percent, or about 80 percent, or about 85 percent, or about 90percent, or about 95, 96, 97, 98, or 99 percent identical to thenucleotide sequence as shown in either SEQ ID NO: 1 or SEQ ID NO: 3.Related nucleic acid molecules encode polypeptides possessing at leastone activity of the polypeptide set forth in either SEQ ID NO: 2 or SEQID NO: 4.

Differences in the nucleic acid sequence may result in conservativeand/or non-conservative modifications of the amino acid sequencerelative to the amino acid sequence of either SEQ ID NO: 2 or SEQ ID NO:4.

Conservative modifications to the amino acid sequence of either SEQ IDNO: 2 or SEQ ID NO: 4 (and the corresponding modifications to theencoding nucleotides) will produce a polypeptide having functional andchemical characteristics similar to those of TEM5α polypeptides. Incontrast, substantial modifications in the functional and/or chemicalcharacteristics of TEM5α polypeptides may be accomplished by selectingsubstitutions in the amino acid sequence of either SEQ ID NO: 2 or SEQID NO: 4 that differ significantly in their effect on maintaining (a)the structure of the molecular backbone in the area of the substitution,for example, as a sheet or helical conformation, (b) the charge orhydrophobicity of the molecule at the target site, or (c) the bulk ofthe side chain.

For example, a “conservative amino acid substitution” may involve asubstitution of a native amino acid residue with a normative residuesuch that there is little or no effect on the polarity or charge of theamino acid residue at that position. Furthermore, any native residue inthe polypeptide may also be substituted with alanine, as has beenpreviously described for “alanine scanning mutagenesis.”

Conservative amino acid substitutions also encompass non-naturallyoccurring amino acid residues that are typically incorporated bychemical peptide synthesis rather than by synthesis in biologicalsystems. These include peptidomimetics, and other reversed or invertedforms of amino acid moieties.

Naturally occurring residues may be divided into classes based on commonside chain properties:

1) hydrophobic: norleucine, Met, Ala, Val, Leu, Ile;

2) neutral hydrophilic: Cys, Ser, Thr;

3) acidic: Asp, Glu;

4) basic: Asn, Gln, His, Lys, Arg;

5) residues that influence chain orientation: Gly, Pro; and

6) aromatic: Trp, Tyr, Phe.

For example, non-conservative substitutions may involve the exchange ofa member of one of these classes for a member from another class. Suchsubstituted residues may be introduced into regions of the human TEM5αpolypeptide that are homologous with non-human TEM5α polypeptides, orinto the non-homologous regions of the molecule.

In making such changes, the hydropathic index of amino acids may beconsidered. Each amino acid has been assigned a hydropathic index on thebasis of its hydrophobicity and charge characteristics. The hydropathicindices are: isoleucine (+4.5); valine (+4.2); leucine (+3.8);phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9);alanine (+1.8); glycine (−0.4); threonine (−0.7); serine (−0.8);tryptophan (−0.9); tyrosine (−1.3); proline (−1.6); histidine (−3.2);glutamate (−3.5); glutamine (−3.5); aspartate (−3.5); asparagine (−3.5);lysine (−3.9); and arginine (−4.5).

The importance of the hydropathic amino acid index in conferringinteractive biological function on a protein is generally understood inthe art (Kyte et al., 1982, J. Mol. Biol. 157:105-31). It is known thatcertain amino acids may be substituted for other amino acids having asimilar hydropathic index or score and still retain a similar biologicalactivity. In making changes based upon the hydropathic index, thesubstitution of amino acids whose hydropathic indices are within ±2 ispreferred, those within ±1 are particularly preferred, and those within±0.5 are even more particularly preferred.

It is also understood in the art that the substitution of like aminoacids can be made effectively on the basis of hydrophilicity,particularly where the biologically functionally equivalent protein orpeptide thereby created is intended for use in immunologicalembodiments, as in the present case. The greatest local averagehydrophilicity of a protein, as governed by the hydrophilicity of itsadjacent amino acids, correlates with its immunogenicity andantigenicity, i.e., with a biological property of the protein.

The following hydrophilicity values have been assigned to these aminoacid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0±1);glutamate (+3.0±1); serine (+0.3); asparagine (+0.2); glutamine (+0.2);glycine (0); threonine (−0.4); proline (−0.5±1); alanine (−0.5);histidine (−0.5); cysteine (−1.0); methionine (−1.3); valine (−1.5);leucine (−1.8); isoleucine (−1.8); tyrosine (−2.3); phenylalanine(−2.5); and tryptophan (−3.4). In making changes based upon similarhydrophilicity values, the substitution of amino acids whosehydrophilicity values are within ±2 is preferred, those within ±1 areparticularly preferred, and those within ±0.5 are even more particularlypreferred. One may also identify epitopes from primary amino acidsequences on the basis of hydrophilicity. These regions are alsoreferred to as “epitopic core regions.”

Desired amino acid substitutions (whether conservative ornon-conservative) can be determined by those skilled in the art at thetime such substitutions are desired. For example, amino acidsubstitutions can be used to identify important residues of the TEM5αpolypeptide, or to increase or decrease the affinity of the TEM5αpolypeptides described herein. Exemplary amino acid substitutions areset forth in Table I.

TABLE I Amino Acid Substitutions Original Residues ExemplarySubstitutions Preferred Substitutions Ala Val, Leu, Ile Val Arg Lys,Gln, Asn Lys Asn Gln Gln Asp Glu Glu Cys Ser, Ala Ser Gln Asn Asn GluAsp Asp Gly Pro, Ala Ala His Asn, Gln, Lys, Arg Arg Ile Leu, Val, Met,Ala, Leu Phe, Norleucine Leu Norleucine, Ile, Ile Val, Met, Ala, Phe LysArg, 1,4 Diamino-butyric Arg Acid, Gln, Asn Met Leu, Phe, Ile Leu PheLeu, Val, Ile, Ala, Leu Tyr Pro Ala Gly Ser Thr, Ala, Cys Thr Thr SerSer Trp Tyr, Phe Tyr Tyr Trp, Phe, Thr, Ser Phe Val Ile, Met, Leu, Phe,Leu Ala, Norleucine

A skilled artisan will be able to determine suitable variants of thepolypeptide as set forth in either SEQ ID NO: 2 or SEQ ID NO: 4 usingwell-known techniques. For identifying suitable areas of the moleculethat may be changed without destroying biological activity, one skilledin the art may target areas not believed to be important for activity.For example, when similar polypeptides with similar activities from thesame species or from other species are known, one skilled in the art maycompare the amino acid sequence of a TEM5α polypeptide to such similarpolypeptides. With such a comparison, one can identify residues andportions of the molecules that are conserved among similar polypeptides.It will be appreciated that changes in areas of the TEM5α molecule thatare not conserved relative to such similar polypeptides would be lesslikely to adversely affect the biological activity and/or structure of aTEM5α polypeptide. One skilled in the art would also know that, even inrelatively conserved regions, one may substitute chemically similaramino acids for the naturally occurring residues while retainingactivity (conservative amino acid residue substitutions). Therefore,even areas that may be important for biological activity or forstructure may be subject to conservative amino acid substitutionswithout destroying the biological activity or without adverselyaffecting the polypeptide structure.

Additionally, one skilled in the art can review structure-functionstudies identifying residues in similar polypeptides that are importantfor activity or structure. In view of such a comparison, one can predictthe importance of amino acid residues in a TEM5α polypeptide thatcorrespond to amino acid residues that are important for activity orstructure in similar polypeptides. One skilled in the art may opt forchemically similar amino acid substitutions for such predicted importantamino acid residues of TEM5α polypeptides.

One skilled in the art can also analyze the three-dimensional structureand amino acid sequence in relation to that structure in similarpolypeptides. In view of such information, one skilled in the art maypredict the alignment of amino acid residues of TEM5α polypeptide withrespect to its three dimensional structure. One skilled in the art maychoose not to make radical changes to amino acid residues predicted tobe on the surface of the protein, since such residues may be involved inimportant interactions with other molecules. Moreover, one skilled inthe art may generate test variants containing a single amino acidsubstitution at each amino acid residue. The variants could be screenedusing activity assays known to those with skill in the art. Suchvariants could be used to gather information about suitable variants.For example, if one discovered that a change to a particular amino acidresidue resulted in destroyed, undesirably reduced, or unsuitableactivity, variants with such a change would be avoided. In other words,based on information gathered from such routine experiments, one skilledin the art can readily determine the amino acids where furthersubstitutions should be avoided either alone or in combination withother mutations.

A number of scientific publications have been devoted to the predictionof secondary structure. See Moult, 1996, Curr. Opin. Biotechnol.7:422-27; Chou et al., 1974, Biochemistry 13:222-45; Chou et al., 1974,Biochemistry 113:211-22; Chou et al., 1978, Adv. Enzymol. Relat. AreasMol. Biol. 47:45-48; Chou et al., 1978, Ann. Rev. Biochem. 47:251-276;and Chou et al., 1979, Biophys. J. 26:367-84. Moreover, computerprograms are currently available to assist with predicting secondarystructure. One method of predicting secondary structure is based uponhomology modeling. For example, two polypeptides or proteins that have asequence identity of greater than 30%, or similarity greater than 40%,often have similar structural topologies. The recent growth of theprotein structural database (PDB) has provided enhanced predictabilityof secondary structure, including the potential number of folds withinthe structure of a polypeptide or protein. See Holm et al., 1999,Nucleic Acids Res. 27:244-47. It has been suggested that there are alimited number of folds in a given polypeptide or protein and that oncea critical number of structures have been resolved, structuralprediction will become dramatically more accurate (Brenner et al., 1997,Curr. Opin. Struct. Biol. 7:369-76).

Additional methods of predicting secondary structure include “threading”(Jones, 1997, Curr. Opin. Struct. Biol. 7:377-87; Sippl et al., 1996,Structure 4:15-19), “profile analysis” (Bowie et al., 1991, Science,253:164-70; Gribskov et al., 1990, Methods Enzymol. 183:146-59; Gribskovet al., 1987, Proc. Nat. Acad. Sci. U.S.A. 84:4355-58), and“evolutionary linkage” (See Holm et al., supra, and Brenner et al.,supra).

Preferred TEM5α polypeptide variants include glycosylation variantswherein the number and/or type of glycosylation sites have been alteredcompared to the amino acid sequence set forth in either SEQ ID NO: 2 orSEQ ID NO: 4. In one embodiment, TEM5α polypeptide variants comprise agreater or a lesser number of N-linked glycosylation sites than theamino acid sequence set forth in either SEQ ID NO: 2 or SEQ ID NO: 4. AnN-linked glycosylation site is characterized by the sequence: Asn-X-Seror Asn-X-Thr, wherein the amino acid residue designated as X may be anyamino acid residue except proline. The substitution of amino acidresidues to create this sequence provides a potential new site for theaddition of an N-linked carbohydrate chain. Alternatively, substitutionsthat eliminate this sequence will remove an existing N-linkedcarbohydrate chain. Also provided is a rearrangement of N-linkedcarbohydrate chains wherein one or more N-linked glycosylation sites(typically those that are naturally occurring) are eliminated and one ormore new N-linked sites are created. Additional preferred TEM5α variantsinclude cysteine variants, wherein one or more cysteine residues aredeleted or substituted with another amino acid (e.g., serine) ascompared to the amino acid sequence set forth in either SEQ ID NO: 2 orSEQ ID NO: 4. Cysteine variants are useful when TEM5α polypeptides mustbe refolded into a biologically active conformation such as after theisolation of insoluble inclusion bodies. Cysteine variants generallyhave fewer cysteine residues than the native protein, and typically havean even number to minimize interactions resulting from unpairedcysteines.

In other embodiments, TEM5α polypeptide variants comprise an amino acidsequence as set forth in either SEQ ID NO: 2 or SEQ ID NO: 4 with atleast one amino acid insertion and wherein the polypeptide has anactivity of the polypeptide set forth in either SEQ ID NO: 2 or SEQ IDNO: 4, or an amino acid sequence encoding a polypeptide as set forth ineither SEQ ID NO: 2 or SEQ ID NO: 4 with at least one amino aciddeletion and wherein the polypeptide has an activity of the polypeptideset forth in either SEQ ID NO: 2 or SEQ ID NO: 4. TEM5α polypeptidevariants also comprise an amino acid sequence as set forth in either SEQID NO: 2 or SEQ ID NO: 4 wherein the polypeptide has a carboxyl- and/oramino-terminal truncation and further wherein the polypeptide has anactivity of the polypeptide set forth in either SEQ ID NO: 2 or SEQ IDNO: 4. TEM5α polypeptide variants further comprise an amino acidsequence as set forth in either SEQ ID NO: 2 or SEQ ID NO: 4 with atleast one modification that is an amino acid substitution, amino acidinsertion, amino acid deletion, carboxyl-terminal truncation, oramino-terminal truncation, and wherein the polypeptide has an activityof the polypeptide set forth in either SEQ ID NO: 2 or SEQ ID NO: 4.

In further embodiments, TEM5α polypeptide variants comprise an aminoacid sequence that is at least about 70 percent identical to the aminoacid sequence as set forth in either SEQ ID NO: 2 or SEQ ID NO: 4. Inpreferred embodiments, TEM5α polypeptide variants comprise an amino acidsequence that is at least about 75 percent, or about 80 percent, orabout 85 percent, or about 90 percent, or about 95, 96, 97, 98, or 99percent identical to the amino acid sequence as set forth in either SEQID NO: 2 or SEQ ID NO: 4. TEM5α polypeptide variants possess at leastone activity of the polypeptide set forth in either SEQ ID NO: 2 or SEQID NO: 4.

In addition, the polypeptide comprising the amino acid sequence ofeither SEQ ID NO: 2 or SEQ ID NO: 4, or other TEM5α polypeptide, may befused to a homologous polypeptide to form a homodimer or to aheterologous polypeptide to form a heterodimer. Heterologous peptidesand polypeptides include, but are not limited to: an epitope to allowfor the detection and/or isolation of a TEM5α fusion polypeptide; atransmembrane receptor protein or a portion thereof, such as anextracellular domain or a transmembrane and intracellular domain; aligand or a portion thereof which binds to a transmembrane receptorprotein; an enzyme or portion thereof which is catalytically active; apolypeptide or peptide which promotes oligomerization, such as a leucinezipper domain; a polypeptide or peptide which increases stability, suchas an immunoglobulin constant region; and a polypeptide which has atherapeutic activity different from the polypeptide comprising the aminoacid sequence as set forth in either SEQ ID NO: 2 or SEQ ID NO: 4, orother TEM5α polypeptide.

Fusions can be made either at the amino-terminus or at thecarboxyl-terminus of the polypeptide comprising the amino acid sequenceset forth in either SEQ ID NO: 2 or SEQ ID NO: 4, or other TEM5αpolypeptide. Fusions may be direct with no linker or adapter molecule ormay be through a linker or adapter molecule. A linker or adaptermolecule may be one or more amino acid residues, typically from about 20to about 50 amino acid residues. A linker or adapter molecule may alsobe designed with a cleavage site for a DNA restriction endonuclease orfor a protease to allow for the separation of the fused moieties. Itwill be appreciated that once constructed, the fusion polypeptides canbe derivatized according to the methods described herein.

In a further embodiment of the invention, the polypeptide comprising theamino acid sequence of either SEQ ID NO: 2 or SEQ ID NO: 4, or otherTEM5α polypeptide, is fused to one or more domains of an Fc region ofhuman IgG. Antibodies comprise two functionally independent parts, avariable domain known as “Fab,” that binds an antigen, and a constantdomain known as “Fc,” that is involved in effector functions such ascomplement activation and attack by phagocytic cells. An Fc has a longserum half-life, whereas an Fab is short-lived. Capon et al., 1989,Nature 337:525-31. When constructed together with a therapeutic protein,an Fc domain can provide longer half-life or incorporate such functionsas Fc receptor binding, protein A binding, complement fixation, andperhaps even placental transfer. Id. Table II summarizes the use ofcertain Fc fusions known in the art.

TABLE II Fc Fusion with Therapeutic Proteins Fusion Therapeutic Form ofFc partner implications Reference IgG1 N-terminus Hodgkin's disease;U.S. Pat. No. of CD30-L anaplastic 5,480,981 lymphoma; T-cell leukemiaMurine IL-10 anti-inflammatory; Zheng et al., 1995, Fcγ2a transplant J.Immunol. 154: rejection 5590-600 IgG1 TNF septic shock Fisher et al.,1996, receptor N. Engl. J. Med. 334: 1697-1702; Van Zee et al., 1996, J.Immunol. 156: 2221-30 IgG, IgA, TNF inflammation, U.S. Pat. No. IgM, orIgE receptor autoimmune 5,808,029 (excluding disorders the first domain)IgG1 CD4 AIDS Capon et al., 1989, receptor Nature 337: 525-31 IgG1,N-terminus anti-cancer, Harvill et al., 1995, IgG3 of IL-2 antiviralImmunotech. 1: 95-105 IgG1 C-terminus osteoarthritis; International Pub.No. of OPG bone density WO 97/23614 IgG1 N-terminus anti-obesityInternational Pub. No. of leptin WO 98/28427 Human Ig CTLA-4 autoimmuneLinsley, 1991, Cγ1 disorders J. Exp. Med., 174: 561-69

In one example, a human IgG hinge, CH2, and CH3 region may be fused ateither the amino-terminus or carboxyl-terminus of the TEM5α polypeptidesusing methods known to the skilled artisan. In another example, a humanIgG hinge, CH2, and CH3 region may be fused at either the amino-terminusor carboxyl-terminus of a TEM5α polypeptide fragment (e.g., thepredicted extracellular portion of TEM5α polypeptide).

The resulting TEM5α fusion polypeptide may be purified by use of aProtein A affinity column. Peptides and proteins fused to an Fc regionhave been found to exhibit a substantially greater half-life in vivothan the unfused counterpart. Also, a fusion to an Fc region allows fordimerization/multimerization of the fusion polypeptide. The Fc regionmay be a naturally occurring Fc region, or may be altered to improvecertain qualities, such as therapeutic qualities, circulation time, orreduced aggregation.

Useful modifications of protein therapeutic agents by fusion with the“Fe” domain of an antibody are discussed in detail in U.S. patentapplication Ser. No. 09/428,082 (International Pub. No. WO 99/25044),which is hereby incorporated by reference in its entirety. That patentapplication discusses linkage to a “vehicle” such as polyethylene gycol(PEG), dextran, or an Fc region.

Identity and similarity of related nucleic acid molecules andpolypeptides are readily calculated by known methods. Such methodsinclude, but are not limited to those described in ComputationalMolecular Biology (A. M. Lesk, ed., Oxford University Press 1988);Biocomputing: Informatics and Genome Projects (D. W. Smith, ed.,Academic Press 1993); Computer Analysis of Sequence Data (Part 1, A. M.Griffin and H. G. Griffin, eds., Humana Press 1994); G. von Heijne,Sequence Analysis in Molecular Biology (Academic Press 1987); SequenceAnalysis Primer (M. Gribskov and J. Devereux, eds., M. Stockton Press1991); and Carillo et al., 1988, SIAM J. Applied Math., 48:1073.

Preferred methods to determine identity and/or similarity are designedto give the largest match between the sequences tested. Methods todetermine identity and similarity are described in publicly availablecomputer programs. Preferred computer program methods to determineidentity and similarity between two sequences include, but are notlimited to, the GCG program package, including GAP (Devereux et al.,1984, Nucleic Acids Res. 12:387; Genetics Computer Group, University ofWisconsin, Madison, Wis.), BLASTP, BLASTN, and FASTA (Altschul et al.,1990, J. Mol. Biol. 215:403-10). The BLASTX program is publiclyavailable from the National Center for Biotechnology Information (NCBI)and other sources (Altschul et al., BLAST Manual (NCB NLM NIH, Bethesda,Md.); Altschul et al., 1990, supra). The well-known Smith Watermanalgorithm may also be used to determine identity.

Certain alignment schemes for aligning two amino acid sequences mayresult in the matching of only a short region of the two sequences, andthis small aligned region may have very high sequence identity eventhough there is no significant relationship between the two full-lengthsequences. Accordingly, in a preferred embodiment, the selectedalignment method (GAP program) will result in an alignment that spans atleast 50 contiguous amino acids of the claimed polypeptide.

For example, using the computer algorithm GAP (Genetics Computer Group,University of Wisconsin, Madison, Wis.), two polypeptides for which thepercent sequence identity is to be determined are aligned for optimalmatching of their respective amino acids (the “matched span,” asdetermined by the algorithm). A gap opening penalty (which is calculatedas 3× the average diagonal; the “average diagonal” is the average of thediagonal of the comparison matrix being used; the “diagonal” is thescore or number assigned to each perfect amino acid match by theparticular comparison matrix) and a gap extension penalty (which isusually 0.1× the gap opening penalty), as well as a comparison matrixsuch as PAM 250 or BLOSUM 62 are used in conjunction with the algorithm.A standard comparison matrix is also used by the algorithm (see Dayhoffet al., 5 Atlas of Protein Sequence and Structure (Supp. 3 1978)(PAM250comparison matrix); Henikoff et al., 1992, Proc. Natl. Acad. Sci USA89:10915-19 (BLOSUM 62 comparison matrix)).

Preferred parameters for polypeptide sequence comparison include thefollowing:

Algorithm: Needleman and Wunsch, 1970, J. Mol. Biol. 48:443-53;

Comparison matrix: BLOSUM 62 (Henikoff et al., supra);

Gap Penalty: 12

Gap Length Penalty: 4

Threshold of Similarity: 0

The GAP program is useful with the above parameters. The aforementionedparameters are the default parameters for polypeptide comparisons (alongwith no penalty for end gaps) using the GAP algorithm.

Preferred parameters for nucleic acid molecule sequence comparisoninclude the following:

Algorithm: Needleman and Wunsch, supra;

Comparison matrix: matches=+10, mismatch=0

Gap Penalty: 50

Gap Length Penalty: 3

The GAP program is also useful with the above parameters. Theaforementioned parameters are the default parameters for nucleic acidmolecule comparisons.

Other exemplary algorithms, gap opening penalties, gap extensionpenalties, comparison matrices, and thresholds of similarity may beused, including those set forth in the Program Manual, WisconsinPackage, Version 9, September, 1997. The particular choices to be madewill be apparent to those of skill in the art and will depend on thespecific comparison to be made, such as DNA-to-DNA, protein-to-protein,protein-to-DNA; and additionally, whether the comparison is betweengiven pairs of sequences (in which case GAP or BestFit are generallypreferred) or between one sequence and a large database of sequences (inwhich case FASTA or BLASTA are preferred).

Nucleic Acid Molecules

The nucleic acid molecules encoding a polypeptide comprising the aminoacid sequence of a TEM5α polypeptide can readily be obtained in avariety of ways including, without limitation, chemical synthesis, cDNAor genomic library screening, expression library screening, and/or PCRamplification of cDNA.

Recombinant DNA methods used herein are generally those set forth inSambrook et al., Molecular Cloning: A Laboratory Manual (Cold SpringHarbor Laboratory Press, 1989) and/or Current Protocols in MolecularBiology (Ausubel et al., eds., Green Publishers Inc. and Wiley and Sons1994). The invention provides for nucleic acid molecules as describedherein and methods for obtaining such molecules.

Where a gene encoding the amino acid sequence of a TEM5α polypeptide hasbeen identified from one species, all or a portion of that gene may beused as a probe to identify orthologs or related genes from the samespecies. The probes or primers may be used to screen cDNA libraries fromvarious tissue sources believed to express the TEM5α polypeptide. Inaddition, part or all of a nucleic acid molecule having the sequence asset forth in either SEQ ID NO: 1 or SEQ ID NO: 3 may be used to screen agenomic library to identify and isolate a gene encoding the amino acidsequence of a TEM5α polypeptide. Typically, conditions of moderate orhigh stringency will be employed for screening to minimize the number offalse positives obtained from the screening.

Nucleic acid molecules encoding the amino acid sequence of TEM5αpolypeptides may also be identified by expression cloning which employsthe detection of positive clones based upon a property of the expressedprotein. Typically, nucleic acid libraries are screened by the bindingan antibody or other binding partner (e.g., receptor or ligand) tocloned proteins that are expressed and displayed on a host cell surface.The antibody or binding partner is modified with a detectable label toidentify those cells expressing the desired clone.

Recombinant expression techniques conducted in accordance with thedescriptions set forth below may be followed to produce thesepolynucleotides and to express the encoded polypeptides. For example, byinserting a nucleic acid sequence that encodes the amino acid sequenceof a TEM5α polypeptide into an appropriate vector, one skilled in theart can readily produce large quantities of the desired nucleotidesequence. The sequences can then be used to generate detection probes oramplification primers. Alternatively, a polynucleotide encoding theamino acid sequence of a TEM5α polypeptide can be inserted into anexpression vector. By introducing the expression vector into anappropriate host, the encoded TEM5α polypeptide may be produced in largeamounts.

Another method for obtaining a suitable nucleic acid sequence is thepolymerase chain reaction (PCR). In this method, cDNA is prepared frompoly(A)+RNA or total RNA using the enzyme reverse transcriptase. Twoprimers, typically complementary to two separate regions of cDNAencoding the amino acid sequence of a TEM5α polypeptide, are then addedto the cDNA along with a polymerase such as Taq polymerase, and thepolymerase amplifies the cDNA region between the two primers.

Another means of preparing a nucleic acid molecule encoding the aminoacid sequence of a TEM5α polypeptide is chemical synthesis using methodswell known to the skilled artisan such as those described by Engels etal., 1989, Angew. Chem. Intl. Ed. 28:716-34. These methods include,inter alia, the phosphotriester, phosphoramidite, and H-phosphonatemethods for nucleic acid synthesis. A preferred method for such chemicalsynthesis is polymer-supported synthesis using standard phosphoramiditechemistry. Typically, the DNA encoding the amino acid sequence of aTEM5α polypeptide will be several hundred nucleotides in length. Nucleicacids larger than about 100 nucleotides can be synthesized as severalfragments using these methods. The fragments can then be ligatedtogether to form the full-length nucleotide sequence of a TEM5α gene.Usually, the DNA fragment encoding the amino-terminus of the polypeptidewill have an ATG, which encodes a methionine residue. This methioninemay or may not be present on the mature form of the TEM5α polypeptide,depending on whether the polypeptide produced in the host cell isdesigned to be secreted from that cell. Other methods known to theskilled artisan may be used as well.

In certain embodiments, nucleic acid variants contain codons which havebeen altered for optimal expression of a TEM5α polypeptide in a givenhost cell. Particular codon alterations will depend upon the TEM5αpolypeptide and host cell selected for expression. Such “codonoptimization” can be carried out by a variety of methods, for example,by selecting codons which are preferred for use in highly expressedgenes in a given host cell. Computer algorithms which incorporate codonfrequency tables such as “Eco_high.Cod” for codon preference of highlyexpressed bacterial genes may be used and are provided by the Universityof Wisconsin Package Version 9.0 (Genetics Computer Group, Madison,Wis.). Other useful codon frequency tables include “Celegans_high.cod,”“Celegans_low.cod,” “Drosophila_high.cod,” “Human_high.cod,”“Maize_high.cod,” and “Yeast_high.cod.”

In some cases, it may be desirable to prepare nucleic acid moleculesencoding TEM5α polypeptide variants. Nucleic acid molecules encodingvariants may be produced using site directed mutagenesis, PCRamplification, or other appropriate methods, where the primer(s) havethe desired point mutations (see Sambrook et al., supra, and Ausubel etal., supra, for descriptions of mutagenesis techniques). Chemicalsynthesis using methods described by Engels et al., supra, may also beused to prepare such variants. Other methods known to the skilledartisan may be used as well.

Vectors and Host Cells

A nucleic acid molecule encoding the amino acid sequence of a TEM5αpolypeptide is inserted into an appropriate expression vector usingstandard ligation techniques. The vector is typically selected to befunctional in the particular host cell employed (i.e., the vector iscompatible with the host cell machinery such that amplification of thegene and/or expression of the gene can occur). A nucleic acid moleculeencoding the amino acid sequence of a TEM5α polypeptide may beamplified/expressed in prokaryotic, yeast, insect (baculovirus systems)and/or eukaryotic host cells. Selection of the host cell will depend inpart on whether a TEM5α polypeptide is to be post-translationallymodified (e.g., glycosylated and/or phosphorylated). If so, yeast,insect, or mammalian host cells are preferable. For a review ofexpression vectors, see Meth. Enz., vol. 185 (D. V. Goeddel, ed.,Academic Press 1990).

Typically, expression vectors used in any of the host cells will containsequences for plasmid maintenance and for cloning and expression ofexogenous nucleotide sequences. Such sequences, collectively referred toas “flanking sequences” in certain embodiments will typically includeone or more of the following nucleotide sequences: a promoter, one ormore enhancer sequences, an origin of replication, a transcriptionaltermination sequence, a complete intron sequence containing a donor andacceptor splice site, a sequence encoding a leader sequence forpolypeptide secretion, a ribosome binding site, a polyadenylationsequence, a polylinker region for inserting the nucleic acid encodingthe polypeptide to be expressed, and a selectable marker element. Eachof these sequences is discussed below.

Optionally, the vector may contain a “tag”-encoding sequence, i.e., anoligonucleotide molecule located at the 5′ or 3′ end of the TEM5αpolypeptide coding sequence; the oligonucleotide sequence encodespolyHis (such as hexaHis), or another “tag” such as FLAG, HA(hemaglutinin influenza virus), or myc for which commercially availableantibodies exist. This tag is typically fused to the polypeptide uponexpression of the polypeptide, and can serve as a means for affinitypurification of the TEM5α polypeptide from the host cell. Affinitypurification can be accomplished, for example, by column chromatographyusing antibodies against the tag as an affinity matrix. Optionally, thetag can subsequently be removed from the purified TEM5α polypeptide byvarious means such as using certain peptidases for cleavage.

Flanking sequences may be homologous (i.e., from the same species and/orstrain as the host cell), heterologous (i.e., from a species other thanthe host cell species or strain), hybrid (i.e., a combination offlanking sequences from more than one source), or synthetic, or theflanking sequences may be native sequences that normally function toregulate TEM5α polypeptide expression. As such, the source of a flankingsequence may be any prokaryotic or eukaryotic organism, any vertebrateor invertebrate organism, or any plant, provided that the flankingsequence is functional in, and can be activated by, the host cellmachinery.

Flanking sequences useful in the vectors of this invention may beobtained by any of several methods well known in the art. Typically,flanking sequences useful herein—other than the TEM5α gene flankingsequences—will have been previously identified by mapping and/or byrestriction endonuclease digestion and can thus be isolated from theproper tissue source using the appropriate restriction endonucleases. Insome cases, the full nucleotide sequence of a flanking sequence may beknown. Here, the flanking sequence may be synthesized using the methodsdescribed herein for nucleic acid synthesis or cloning.

Where all or only a portion of the flanking sequence is known, it may beobtained using PCR and/or by screening a genomic library with a suitableoligonucleotide and/or flanking sequence fragment from the same oranother species. Where the flanking sequence is not known, a fragment ofDNA containing a flanking sequence may be isolated from a larger pieceof DNA that may contain, for example, a coding sequence or even anothergene or genes. Isolation may be accomplished by restriction endonucleasedigestion to produce the proper DNA fragment followed by isolation usingagarose gel purification, Qiagen® column chromatography (Chatsworth,Calif.), or other methods known to the skilled artisan. The selection ofsuitable enzymes to accomplish this purpose will be readily apparent toone of ordinary skill in the art.

An origin of replication is typically a part of those prokaryoticexpression vectors purchased commercially, and the origin aids in theamplification of the vector in a host cell. Amplification of the vectorto a certain copy number can, in some cases, be important for theoptimal expression of a TEM5α polypeptide. If the vector of choice doesnot contain an origin of replication site, one may be chemicallysynthesized based on a known sequence, and ligated into the vector. Forexample, the origin of replication from the plasmid pBR322 (New EnglandBiolabs, Beverly, Mass.) is suitable for most gram-negative bacteria andvarious origins (e.g., SV40, polyoma, adenovirus, vesicular stomatitusvirus (VSV), or papillomaviruses such as HPV or BPV) are useful forcloning vectors in mammalian cells. Generally, the origin of replicationcomponent is not needed for mammalian expression vectors (for example,the SV40 origin is often used only because it contains the earlypromoter).

A transcription termination sequence is typically located 3′ of the endof a polypeptide coding region and serves to terminate transcription.Usually, a transcription termination sequence in prokaryotic cells is aG-C rich fragment followed by a poly-T sequence. While the sequence iseasily cloned from a library or even purchased commercially as part of avector, it can also be readily synthesized using methods for nucleicacid synthesis such as those described herein.

A selectable marker gene element encodes a protein necessary for thesurvival and growth of a host cell grown in a selective culture medium.Typical selection marker genes encode proteins that (a) conferresistance to antibiotics or other toxins, e.g., ampicillin,tetracycline, or kanamycin for prokaryotic host cells; (b) complementauxotrophic deficiencies of the cell; or (c) supply critical nutrientsnot available from complex media. Preferred selectable markers are thekanamycin resistance gene, the ampicillin resistance gene, and thetetracycline resistance gene. A neomycin resistance gene may also beused for selection in prokaryotic and eukaryotic host cells.

Other selection genes may be used to amplify the gene that will beexpressed. Amplification is the process wherein genes that are ingreater demand for the production of a protein critical for growth arereiterated in tandem within the chromosomes of successive generations ofrecombinant cells. Examples of suitable selectable markers for mammaliancells include dihydrofolate reductase (DHFR) and thymidine kinase. Themammalian cell transformants are placed under selection pressure whereinonly the transformants are uniquely adapted to survive by virtue of theselection gene present in the vector. Selection pressure is imposed byculturing the transformed cells under conditions in which theconcentration of selection agent in the medium is successively changed,thereby leading to the amplification of both the selection gene and theDNA that encodes a TEM5α polypeptide. As a result, increased quantitiesof TEM5α polypeptide are synthesized from the amplified DNA.

A ribosome binding site is usually necessary for translation initiationof mRNA and is characterized by a Shine-Dalgarno sequence (prokaryotes)or a Kozak sequence (eukaryotes). The element is typically located 3′ tothe promoter and 5′ to the coding sequence of a TEM5α polypeptide to beexpressed. The Shine-Dalgarno sequence is varied but is typically apolypurine (i.e., having a high A-G content). Many Shine-Dalgarnosequences have been identified, each of which can be readily synthesizedusing methods set forth herein and used in a prokaryotic vector.

A leader, or signal, sequence may be used to direct a TEM5α polypeptideout of the host cell. Typically, a nucleotide sequence encoding thesignal sequence is positioned in the coding region of a TEM5α nucleicacid molecule, or directly at the 5′ end of a TEM5α polypeptide codingregion. Many signal sequences have been identified, and any of thosethat are functional in the selected host cell may be used in conjunctionwith a TEM5α nucleic acid molecule. Therefore, a signal sequence may behomologous (naturally occurring) or heterologous to the TEM5α nucleicacid molecule. Additionally, a signal sequence may be chemicallysynthesized using methods described herein. In most cases, the secretionof a TEM5α polypeptide from the host cell via the presence of a signalpeptide will result in the removal of the signal peptide from thesecreted TEM5α polypeptide. The signal sequence may be a component ofthe vector, or it may be a part of a TEM5α nucleic acid molecule that isinserted into the vector.

Included within the scope of this invention is the use of either anucleotide sequence encoding a native TEM5α polypeptide signal sequencejoined to a TEM5α polypeptide coding region or a nucleotide sequenceencoding a heterologous signal sequence joined to a TEM5α polypeptidecoding region. The heterologous signal sequence selected should be onethat is recognized and processed, i.e., cleaved by a signal peptidase,by the host cell. For prokaryotic host cells that do not recognize andprocess the native TEM5α polypeptide signal sequence, the signalsequence is substituted by a prokaryotic signal sequence selected, forexample, from the group of the alkaline phosphatase, penicillinase, orheat-stable enterotoxin II leaders. For yeast secretion, the nativeTEM5α polypeptide signal sequence may be substituted by the yeastinvertase, alpha factor, or acid phosphatase leaders. In mammalian cellexpression the native signal sequence is satisfactory, although othermammalian signal sequences may be suitable.

In some cases, such as where glycosylation is desired in a eukaryotichost cell expression system, one may manipulate the various presequencesto improve glycosylation or yield. For example, one may alter thepeptidase cleavage site of a particular signal peptide, or addpro-sequences, which also may affect glycosylation. The final proteinproduct may have, in the −1 position (relative to the first amino acidof the mature protein) one or more additional amino acids incident toexpression, which may not have been totally removed. For example, thefinal protein product may have one or two amino acid residues found inthe peptidase cleavage site, attached to the amino-terminusAlternatively, use of some enzyme cleavage sites may result in aslightly truncated form of the desired TEM5α polypeptide, if the enzymecuts at such area within the mature polypeptide.

In many cases, transcription of a nucleic acid molecule is increased bythe presence of one or more introns in the vector; this is particularlytrue where a polypeptide is produced in eukaryotic host cells,especially mammalian host cells. The introns used may be naturallyoccurring within the TEM5α gene especially where the gene used is afull-length genomic sequence or a fragment thereof. Where the intron isnot naturally occurring within the gene (as for most cDNAs), the intronmay be obtained from another source. The position of the intron withrespect to flanking sequences and the TEM5α gene is generally important,as the intron must be transcribed to be effective. Thus, when a TEM5αcDNA molecule is being transcribed, the preferred position for theintron is 3′ to the transcription start site and 5′ to the poly-Atranscription termination sequence. Preferably, the intron or intronswill be located on one side or the other (i.e., 5′ or 3′) of the cDNAsuch that it does not interrupt the coding sequence. Any intron from anysource, including viral, prokaryotic and eukaryotic (plant or animal)organisms, may be used to practice this invention, provided that it iscompatible with the host cell into which it is inserted. Also includedherein are synthetic introns. Optionally, more than one intron may beused in the vector.

The expression and cloning vectors of the present invention willtypically contain a promoter that is recognized by the host organism andoperably linked to the molecule encoding the TEM5α polypeptide.Promoters are untranscribed sequences located upstream (i.e., 5′) to thestart codon of a structural gene (generally within about 100 to 1000 bp)that control the transcription of the structural gene. Promoters areconventionally grouped into one of two classes: inducible promoters andconstitutive promoters. Inducible promoters initiate increased levels oftranscription from DNA under their control in response to some change inculture conditions, such as the presence or absence of a nutrient or achange in temperature. Constitutive promoters, on the other hand,initiate continual gene product production; that is, there is little orno control over gene expression. A large number of promoters, recognizedby a variety of potential host cells, are well known. A suitablepromoter is operably linked to the DNA encoding TEM5α polypeptide byremoving the promoter from the source DNA by restriction enzymedigestion and inserting the desired promoter sequence into the vector.The native TEM5α promoter sequence may be used to direct amplificationand/or expression of a TEM5α nucleic acid molecule. A heterologouspromoter is preferred, however, if it permits greater transcription andhigher yields of the expressed protein as compared to the nativepromoter, and if it is compatible with the host cell system that hasbeen selected for use.

Promoters suitable for use with prokaryotic hosts include thebeta-lactamase and lactose promoter systems; alkaline phosphatase; atryptophan (trp) promoter system; and hybrid promoters such as the tacpromoter. Other known bacterial promoters are also suitable. Theirsequences have been published, thereby enabling one skilled in the artto ligate them to the desired DNA sequence, using linkers or adapters asneeded to supply any useful restriction sites.

Suitable promoters for use with yeast hosts are also well known in theart. Yeast enhancers are advantageously used with yeast promoters.Suitable promoters for use with mammalian host cells are well known andinclude, but are not limited to, those obtained from the genomes ofviruses such as polyoma virus, fowlpox virus, adenovirus (such asAdenovirus 2), bovine papilloma virus, avian sarcoma virus,cytomegalovirus, retroviruses, hepatitis-B virus and most preferablySimian Virus 40 (SV40). Other suitable mammalian promoters includeheterologous mammalian promoters, for example, heat-shock promoters andthe actin promoter.

Additional promoters which may be of interest in controlling TEM5α geneexpression include, but are not limited to: the SV40 early promoterregion (Bernoist and Chambon, 1981, Nature 290:304-10); the CMVpromoter; the promoter contained in the 3′ long terminal repeat of Roussarcoma virus (Yamamoto, et al., 1980, Cell 22:787-97); the herpesthymidine kinase promoter (Wagner et al., 1981, Proc. Natl. Acad. Sci.U.S.A. 78:1444-45); the regulatory sequences of the metallothionine gene(Brinster et al., 1982, Nature 296:39-42); prokaryotic expressionvectors such as the beta-lactamase promoter (VIIIa-Kamaroff et al.,1978, Proc. Natl. Acad. Sci. U.S.A., 75:3727-31); or the tac promoter(DeBoer et al., 1983, Proc. Natl. Acad. Sci. U.S.A., 80:21-25). Also ofinterest are the following animal transcriptional control regions, whichexhibit tissue specificity and have been utilized in transgenic animals:the elastase I gene control region which is active in pancreatic acinarcells (Swift et al., 1984, Cell 38:639-46; Ornitz et al., 1986, ColdSpring Harbor Symp. Quant. Biol. 50:399-409 (1986); MacDonald, 1987,Hepatology 7:425-515); the insulin gene control region which is activein pancreatic beta cells (Hanahan, 1985, Nature 315:115-22); theimmunoglobulin gene control region which is active in lymphoid cells(Grosschedl et al., 1984, Cell 38:647-58; Adames et al., 1985, Nature318:533-38; Alexander et al., 1987, Mol. Cell. Biol., 7:1436-44); themouse mammary tumor virus control region which is active in testicular,breast, lymphoid and mast cells (Leder et al., 1986, Cell 45:485-95);the albumin gene control region which is active in liver (Pinkert etal., 1987, Genes and Devel. 1:268-76); the alpha-feto-protein genecontrol region which is active in liver (Krumlauf et al., 1985, Mol.Cell. Biol., 5:1639-48; Hammer et al., 1987, Science 235:53-58); thealpha 1-antitrypsin gene control region which is active in the liver(Kelsey et al., 1987, Genes and Devel. 1:161-71); the beta-globin genecontrol region which is active in myeloid cells (Mogram et al., 1985,Nature 315:338-40; Kollias et al., 1986, Cell 46:89-94); the myelinbasic protein gene control region which is active in oligodendrocytecells in the brain (Readhead et al., 1987, Cell 48:703-12); the myosinlight chain-2 gene control region which is active in skeletal muscle(Sani, 1985, Nature 314:283-86); and the gonadotropic releasing hormonegene control region which is active in the hypothalamus (Mason et al.,1986, Science 234:1372-78).

An enhancer sequence may be inserted into the vector to increase thetranscription of a DNA encoding a TEM5α polypeptide of the presentinvention by higher eukaryotes. Enhancers are cis-acting elements ofDNA, usually about 10-300 bp in length, that act on the promoter toincrease transcription. Enhancers are relatively orientation andposition independent. They have been found 5′ and 3′ to thetranscription unit. Several enhancer sequences available from mammaliangenes are known (e.g., globin, elastase, albumin, alpha-feto-protein andinsulin). Typically, however, an enhancer from a virus will be used. TheSV40 enhancer, the cytomegalovirus early promoter enhancer, the polyomaenhancer, and adenovirus enhancers are exemplary enhancing elements forthe activation of eukaryotic promoters. While an enhancer may be splicedinto the vector at a position 5′ or 3′ to a TEM5α nucleic acid molecule,it is typically located at a site 5′ from the promoter.

Expression vectors of the invention may be constructed from a startingvector such as a commercially available vector. Such vectors may or maynot contain all of the desired flanking sequences. Where one or more ofthe flanking sequences described herein are not already present in thevector, they may be individually obtained and ligated into the vector.Methods used for obtaining each of the flanking sequences are well knownto one skilled in the art.

Preferred vectors for practicing this invention are those that arecompatible with bacterial, insect, and mammalian host cells. Suchvectors include, inter alia, pCRII, pCR3, and pcDNA3.1 (Invitrogen,Carlsbad, Calif.), pBSII (Stratagene, La Jolla, Calif.), pET15 (Novagen,Madison, Wis.), pGEX (Pharmacia Biotech, Piscataway, N.J.), pEGFP-N2(Clontech, Palo Alto, Calif.), pETL (BlueBacII, Invitrogen), pDSR-alpha(International Pub. No. WO 90/14363) and pFastBacDual (Gibco-BRL, GrandIsland, N.Y.).

Additional suitable vectors include, but are not limited to, cosmids,plasmids, or modified viruses, but it will be appreciated that thevector system must be compatible with the selected host cell. Suchvectors include, but are not limited to plasmids such as Bluescript®plasmid derivatives (a high copy number ColE1-based phagemid; StratageneCloning Systems; La Jolla Calif.), PCR cloning plasmids designed forcloning Taq-amplified PCR products (e.g., TOPO™ TA Cloning® Kit, PCR2.1®plasmid derivatives; Invitrogen), and mammalian, yeast or virus vectorssuch as a baculovirus expression system (pBacPAK plasmid derivatives;Clontech; Palo Alto, Calif.).

After the vector has been constructed and a nucleic acid moleculeencoding a TEM5α polypeptide has been inserted into the proper site ofthe vector, the completed vector may be inserted into a suitable hostcell for amplification and/or polypeptide expression. The transformationof an expression vector for a TEM5α polypeptide into a selected hostcell may be accomplished by well known methods including methods such astransfection, infection, calcium chloride, electroporation,microinjection, lipofection, DEAE-dextran method, or other knowntechniques. The method selected will in part be a function of the typeof host cell to be used. These methods and other suitable methods arewell known to the skilled artisan, and are set forth, for example, inSambrook et al., supra.

Host cells may be prokaryotic host cells (such as E. coli) or eukaryotichost cells (such as a yeast, insect, or vertebrate cell). The host cell,when cultured under appropriate conditions, synthesizes a TEM5αpolypeptide that can subsequently be collected from the culture medium(if the host cell secretes it into the medium) or directly from the hostcell producing it (if it is not secreted). The selection of anappropriate host cell will depend upon various factors, such as desiredexpression levels, polypeptide modifications that are desirable ornecessary for activity (such as glycosylation or phosphorylation) andease of folding into a biologically active molecule.

A number of suitable host cells are known in the art and many areavailable from the American Type Culture Collection (ATCC), Manassas,Va. Examples include, but are not limited to, mammalian cells, such asChinese hamster ovary cells (CHO), CHO DHFR(−) cells (Urlaub et al.,1980, Proc. Natl. Acad. Sci. U.S.A. 97:4216-20), human embryonic kidney(HEK) 293 or 293T cells, or 3T3 cells. The selection of suitablemammalian host cells and methods for transformation, culture,amplification, screening, product production, and purification are knownin the art. Other suitable mammalian cell lines, are the monkey COS-1and COS-7 cell lines, and the CV-1 cell line. Further exemplarymammalian host cells include primate cell lines and rodent cell lines,including transformed cell lines. Normal diploid cells, cell strainsderived from in vitro culture of primary tissue, as well as primaryexplants, are also suitable. Candidate cells may be genotypicallydeficient in the selection gene, or may contain a dominantly actingselection gene. Other suitable mammalian cell lines include but are notlimited to, mouse neuroblastoma N2A cells, HeLa, mouse L-929 cells, 3T3lines derived from Swiss, Balb-c or NIH mice, BHK or HaK hamster celllines. Each of these cell lines is known by and available to thoseskilled in the art of protein expression.

Similarly useful as host cells suitable for the present invention arebacterial cells. For example, the various strains of E. coli (e.g.,HB101, DH5α, DH10, and MC1061) are well-known as host cells in the fieldof biotechnology. Various strains of B. subtilis, Pseudomonas spp.,other Bacillus spp., Streptomyces spp., and the like may also beemployed in this method.

Many strains of yeast cells known to those skilled in the art are alsoavailable as host cells for the expression of the polypeptides of thepresent invention. Preferred yeast cells include, for example,Saccharomyces cerivisae and Pichia pastoris.

Additionally, where desired, insect cell systems may be utilized in themethods of the present invention. Such systems are described, forexample, in Kitts et al., 1993, Biotechniques, 14:810-17; Lucklow, 1993,Curr. Opin. Biotechnol. 4:564-72; and Lucklow et al., 1993, J. Virol.,67:4566-79. Preferred insect cells are Sf-9 and Hi5 (Invitrogen).

One may also use transgenic animals to express glycosylated TEM5αpolypeptides. For example, one may use a transgenic milk-producinganimal (a cow or goat, for example) and obtain the present glycosylatedpolypeptide in the animal milk. One may also use plants to produce TEM5αpolypeptides, however, in general, the glycosylation occurring in plantsis different from that produced in mammalian cells, and may result in aglycosylated product which is not suitable for human therapeutic use.

Polypeptide Production

Host cells comprising a TEM5α polypeptide expression vector may becultured using standard media well known to the skilled artisan. Themedia will usually contain all nutrients necessary for the growth andsurvival of the cells. Suitable media for culturing E. coli cellsinclude, for example, Luria Broth (LB) and/or Terrific Broth (TB).Suitable media for culturing eukaryotic cells include Roswell ParkMemorial Institute medium 1640 (RPMI 1640), Minimal Essential Medium(MEM) and/or Dulbecco's Modified Eagle Medium (DMEM), all of which maybe supplemented with serum and/or growth factors as necessary for theparticular cell line being cultured. A suitable medium for insectcultures is Grace's medium supplemented with yeastolate, lactalbuminhydrolysate, and/or fetal calf serum as necessary.

Typically, an antibiotic or other compound useful for selective growthof transfected or transformed cells is added as a supplement to themedia. The compound to be used will be dictated by the selectable markerelement present on the plasmid with which the host cell was transformed.For example, where the selectable marker element is kanamycinresistance, the compound added to the culture medium will be kanamycin.Other compounds for selective growth include ampicillin, tetracycline,and neomycin.

The amount of a TEM5α polypeptide produced by a host cell can beevaluated using standard methods known in the art. Such methods include,without limitation, Western blot analysis, SDS-polyacrylamide gelelectrophoresis, non-denaturing gel electrophoresis, High PerformanceLiquid Chromatography (HPLC) separation, immunoprecipitation, and/oractivity assays such as DNA binding gel shift assays.

If a TEM5α polypeptide has been designed to be secreted from the hostcells, the majority of polypeptide may be found in the cell culturemedium. If however, the TEM5α polypeptide is not secreted from the hostcells, it will be present in the cytoplasm and/or the nucleus (foreukaryotic host cells) or in the cytosol (for gram-negative bacteriahost cells).

For a TEM5α polypeptide situated in the host cell cytoplasm and/ornucleus (for eukaryotic host cells) or in the cytosol (for bacterialhost cells), the intracellular material (including inclusion bodies forgram-negative bacteria) can be extracted from the host cell using anystandard technique known to the skilled artisan. For example, the hostcells can be lysed to release the contents of the periplasm/cytoplasm byFrench press, homogenization, and/or sonication followed bycentrifugation.

If a TEM5α polypeptide has formed inclusion bodies in the cytosol, theinclusion bodies can often bind to the inner and/or outer cellularmembranes and thus will be found primarily in the pellet material aftercentrifugation. The pellet material can then be treated at pH extremesor with a chaotropic agent such as a detergent, guanidine, guanidinederivatives, urea, or urea derivatives in the presence of a reducingagent such as dithiothreitol at alkaline pH or tris carboxyethylphosphine at acid pH to release, break apart, and solubilize theinclusion bodies. The solubilized TEM5α polypeptide can then be analyzedusing gel electrophoresis, immunoprecipitation, or the like. If it isdesired to isolate the TEM5α polypeptide, isolation may be accomplishedusing standard methods such as those described herein and in Marston etal., 1990, Meth. Enz., 182:264-75.

In some cases, a TEM5α polypeptide may not be biologically active uponisolation. Various methods for “refolding” or converting the polypeptideto its tertiary structure and generating disulfide linkages can be usedto restore biological activity. Such methods include exposing thesolubilized polypeptide to a pH usually above 7 and in the presence of aparticular concentration of a chaotrope. The selection of chaotrope isvery similar to the choices used for inclusion body solubilization, butusually the chaotrope is used at a lower concentration and is notnecessarily the same as chaotropes used for the solubilization. In mostcases the refolding/oxidation solution will also contain a reducingagent or the reducing agent plus its oxidized form in a specific ratioto generate a particular redox potential allowing for disulfideshuffling to occur in the formation of the protein's cysteine bridges.Some of the commonly used redox couples include cysteine/cystamine,glutathione (GSH)/dithiobis GSH, cupric chloride,dithiothreitol(DTT)/dithiane DTT, and2-2-mercaptoethanol(bME)/dithio-b(ME). In many instances, a cosolventmay be used or may be needed to increase the efficiency of therefolding, and the more common reagents used for this purpose includeglycerol, polyethylene glycol of various molecular weights, arginine andthe like.

If inclusion bodies are not formed to a significant degree uponexpression of a TEM5α polypeptide, then the polypeptide will be foundprimarily in the supernatant after centrifugation of the cellhomogenate. The polypeptide may be further isolated from the supernatantusing methods such as those described herein.

The purification of a TEM5α polypeptide from solution can beaccomplished using a variety of techniques. If the polypeptide has beensynthesized such that it contains a tag such as Hexahistidine (TEM5αpolypeptide/hexaHis) or other small peptide such as FLAG (Eastman KodakCo., New Haven, Conn.) or myc (Invitrogen) at either its carboxyl- oramino-terminus, it may be purified in a one-step process by passing thesolution through an affinity column where the column matrix has a highaffinity for the tag.

For example, polyhistidine binds with great affinity and specificity tonickel. Thus, an affinity column of nickel (such as the Qiagen® nickelcolumns) can be used for purification of TEM5α polypeptide/polyHis. See,e.g., Current Protocols in Molecular Biology §10.11.8 (Ausubel et al.,eds., Green Publishers Inc. and Wiley and Sons 1993).

Additionally, TEM5α polypeptides may be purified through the use of amonoclonal antibody that is capable of specifically recognizing andbinding to a TEM5α polypeptide.

Other suitable procedures for purification include, without limitation,affinity chromatography, immunoaffinity chromatography, ion exchangechromatography, molecular sieve chromatography, HPLC, electrophoresis(including native gel electrophoresis) followed by gel elution, andpreparative isoelectric focusing (“Isoprime” machine/technique, HoeferScientific, San Francisco, Calif.). In some cases, two or morepurification techniques may be combined to achieve increased purity.

TEM5α polypeptides may also be prepared by chemical synthesis methods(such as solid phase peptide synthesis) using techniques known in theart such as those set forth by Merrifield et al., 1963, J. Am. Chem.Soc. 85:2149; Houghten et al., 1985, Proc Natl Acad. Sci. USA 82:5132;and Stewart and Young, Solid Phase Peptide Synthesis (Pierce ChemicalCo. 1984). Such polypeptides may be synthesized with or without amethionine on the amino-terminus Chemically synthesized TEM5αpolypeptides may be oxidized using methods set forth in these referencesto form disulfide bridges. Chemically synthesized TEM5α polypeptides areexpected to have comparable biological activity to the correspondingTEM5α polypeptides produced recombinantly or purified from naturalsources, and thus may be used interchangeably with a recombinant ornatural TEM5α polypeptide.

Another means of obtaining TEM5α polypeptide is via purification frombiological samples such as source tissues and/or fluids in which theTEM5α polypeptide is naturally found. Such purification can be conductedusing methods for protein purification as described herein. The presenceof the TEM5α polypeptide during purification may be monitored, forexample, using an antibody prepared against recombinantly produced TEM5αpolypeptide or peptide fragments thereof.

A number of additional methods for producing nucleic acids andpolypeptides are known in the art, and the methods can be used toproduce polypeptides having specificity for TEM5α polypeptide. See,e.g., Roberts et al., 1997, Proc. Natl. Acad. Sci. U.S.A. 94:12297-303,which describes the production of fusion proteins between an mRNA andits encoded peptide. See also, Roberts, 1999, Curr. Opin. Chem. Biol.3:268-73. Additionally, U.S. Pat. No. 5,824,469 describes methods forobtaining oligonucleotides capable of carrying out a specific biologicalfunction. The procedure involves generating a heterogeneous pool ofoligonucleotides, each having a 5′ randomized sequence, a centralpreselected sequence, and a 3′ randomized sequence. The resultingheterogeneous pool is introduced into a population of cells that do notexhibit the desired biological function. Subpopulations of the cells arethen screened for those that exhibit a predetermined biologicalfunction. From that subpopulation, oligonucleotides capable of carryingout the desired biological function are isolated.

U.S. Pat. Nos. 5,763,192; 5,814,476; 5,723,323; and 5,817,483 describeprocesses for producing peptides or polypeptides. This is done byproducing stochastic genes or fragments thereof, and then introducingthese genes into host cells which produce one or more proteins encodedby the stochastic genes. The host cells are then screened to identifythose clones producing peptides or polypeptides having the desiredactivity.

Another method for producing peptides or polypeptides is described inInternational Pub. No. WO99/15650, filed by Athersys, Inc. Known as“Random Activation of Gene Expression for Gene Discovery” (RAGE-GD), theprocess involves the activation of endogenous gene expression orover-expression of a gene by in situ recombination methods. For example,expression of an endogenous gene is activated or increased byintegrating a regulatory sequence into the target cell that is capableof activating expression of the gene by non-homologous or illegitimaterecombination. The target DNA is first subjected to radiation, and agenetic promoter inserted. The promoter eventually locates a break atthe front of a gene, initiating transcription of the gene. This resultsin expression of the desired peptide or polypeptide.

It will be appreciated that these methods can also be used to createcomprehensive TEM5α polypeptide expression libraries, which cansubsequently be used for high throughput phenotypic screening in avariety of assays, such as biochemical assays, cellular assays, andwhole organism assays (e.g., plant, mouse, etc.).

Synthesis

It will be appreciated by those skilled in the art that the nucleic acidand polypeptide molecules described herein may be produced byrecombinant and other means.

Selective Binding Agents

The term “selective binding agent” refers to a molecule that hasspecificity for one or more TEM5α polypeptides. Suitable selectivebinding agents include, but are not limited to, antibodies andderivatives thereof, polypeptides, and small molecules. Suitableselective binding agents may be prepared using methods known in the art.An exemplary TEM5α polypeptide selective binding agent of the presentinvention is capable of binding a certain portion of the TEM5αpolypeptide thereby inhibiting the binding of the polypeptide to a TEM5αpolypeptide receptor.

Selective binding agents such as antibodies and antibody fragments thatbind TEM5α polypeptides are within the scope of the present invention.The antibodies may be polyclonal including monospecific polyclonal;monoclonal (MAbs); recombinant; chimeric; humanized, such ascomplementarity-determining region (CDR)-grafted; human; single chain;and/or bispecific; as well as fragments; variants; or derivativesthereof. Antibody fragments include those portions of the antibody thatbind to an epitope on the TEM5α polypeptide. Examples of such fragmentsinclude Fab and F(ab′) fragments generated by enzymatic cleavage offull-length antibodies. Other binding fragments include those generatedby recombinant DNA techniques, such as the expression of recombinantplasmids containing nucleic acid sequences encoding antibody variableregions.

Polyclonal antibodies directed toward a TEM5α polypeptide generally areproduced in animals (e.g., rabbits or mice) by means of multiplesubcutaneous or intraperitoneal injections of TEM5α polypeptide and anadjuvant. It may be useful to conjugate a TEM5α polypeptide to a carrierprotein that is immunogenic in the species to be immunized, such askeyhole limpet hemocyanin, serum, albumin, bovine thyroglobulin, orsoybean trypsin inhibitor. Also, aggregating agents such as alum areused to enhance the immune response. After immunization, the animals arebled and the serum is assayed for anti-TEM5α antibody titer.

Monoclonal antibodies directed toward TEM5α polypeptides are producedusing any method that provides for the production of antibody moleculesby continuous cell lines in culture. Examples of suitable methods forpreparing monoclonal antibodies include the hybridoma methods of Kohleret al., 1975, Nature 256:495-97 and the human B-cell hybridoma method(Kozbor, 1984, J. Immunol. 133:3001; Brodeur et al., Monoclonal AntibodyProduction Techniques and Applications 51-63 (Marcel Dekker, Inc.,1987). Also provided by the invention are hybridoma cell lines thatproduce monoclonal antibodies reactive with TEM5α polypeptides.

Monoclonal antibodies of the invention may be modified for use astherapeutics. One embodiment is a “chimeric” antibody in which a portionof the heavy (H) and/or light (L) chain is identical with or homologousto a corresponding sequence in antibodies derived from a particularspecies or belonging to a particular antibody class or subclass, whilethe remainder of the chain(s) is/are identical with or homologous to acorresponding sequence in antibodies derived from another species orbelonging to another antibody class or subclass. Also included arefragments of such antibodies, so long as they exhibit the desiredbiological activity. See U.S. Pat. No. 4,816,567; Morrison et al., 1985,Proc. Natl. Acad. Sci. 81:6851-55.

In another embodiment, a monoclonal antibody of the invention is a“humanized” antibody. Methods for humanizing non-human antibodies arewell known in the art. See U.S. Pat. Nos. 5,585,089 and 5,693,762.Generally, a humanized antibody has one or more amino acid residuesintroduced into it from a source that is non-human. Humanization can beperformed, for example, using methods described in the art (Jones etal., 1986, Nature 321:522-25; Riechmann et al., 1998, Nature 332:323-27;Verhoeyen et al., 1988, Science 239:1534-36), by substituting at least aportion of a rodent complementarity-determining region for thecorresponding regions of a human antibody.

Also encompassed by the invention are human antibodies that bind TEM5αpolypeptides. Using transgenic animals (e.g., mice) that are capable ofproducing a repertoire of human antibodies in the absence of endogenousimmunoglobulin production such antibodies are produced by immunizationwith a TEM5α polypeptide antigen (i.e., having at least 6 contiguousamino acids), optionally conjugated to a carrier. See, e.g., Jakobovitset al., 1993, Proc. Natl. Acad. Sci. 90:2551-55; Jakobovits et al.,1993, Nature 362:255-58; Bruggermann et al., 1993, Year in Immuno. 7:33.In one method, such transgenic animals are produced by incapacitatingthe endogenous loci encoding the heavy and light immunoglobulin chainstherein, and inserting loci encoding human heavy and light chainproteins into the genome thereof. Partially modified animals, that isanimals having less than the full complement of modifications, are thencross-bred to obtain an animal having all of the desired immune systemmodifications. When administered an immunogen, these transgenic animalsproduce antibodies with human (rather than, e.g., murine) amino acidsequences, including variable regions that are immunospecific for theseantigens. See International Pub. Nos. WO 96/33735 and WO 94/02602.Additional methods are described in U.S. Pat. No. 5,545,807,International Pub. Nos. WO 91/10741 and WO 90/04036, and in EuropeanPatent Nos. 546073B1 and 546073A1. Human antibodies can also be producedby the expression of recombinant DNA in host cells or by expression inhybridoma cells as described herein.

In an alternative embodiment, human antibodies can also be produced fromphage-display libraries (Hoogenboom et al., 1991, J. Mol. Biol. 227:381;Marks et al., 1991, J. Mol. Biol. 222:581). These processes mimic immuneselection through the display of antibody repertoires on the surface offilamentous bacteriophage, and subsequent selection of phage by theirbinding to an antigen of choice. One such technique is described inInternational Pub. No. WO 99/10494, which describes the isolation ofhigh affinity and functional agonistic antibodies for MPL- andmsk-receptors using such an approach.

Chimeric, CDR grafted, and humanized antibodies are typically producedby recombinant methods. Nucleic acids encoding the antibodies areintroduced into host cells and expressed using materials and proceduresdescribed herein. In a preferred embodiment, the antibodies are producedin mammalian host cells, such as CHO cells. Monoclonal (e.g., human)antibodies may be produced by the expression of recombinant DNA in hostcells or by expression in hybridoma cells as described herein.

The anti-TEM5α antibodies of the invention may be employed in any knownassay method, such as competitive binding assays, direct and indirectsandwich assays, and immunoprecipitation assays (Sola, MonoclonalAntibodies: A Manual of Techniques 147-158 (CRC Press, Inc., 1987)) forthe detection and quantitation of TEM5α polypeptides. The antibodieswill bind TEM5α polypeptides with an affinity that is appropriate forthe assay method being employed.

For diagnostic applications, in certain embodiments, anti-TEM5αantibodies may be labeled with a detectable moiety. The detectablemoiety can be any one that is capable of producing, either directly orindirectly, a detectable signal. For example, the detectable moiety maybe a radioisotope, such as ³H, ¹⁴C, ³²P, ³⁵S, ¹²⁵I, ⁹⁹Tc, ¹¹¹In, or⁶⁷Ga; a fluorescent or chemiluminescent compound, such as fluoresceinisothiocyanate, rhodamine, or luciferin; or an enzyme, such as alkalinephosphatase, β-galactosidase, or horseradish peroxidase (Bayer, et al.,1990, Meth. Enz. 184: 138-63).

Competitive binding assays rely on the ability of a labeled standard(e.g., a TEM5α polypeptide, or an immunologically reactive portionthereof) to compete with the test sample analyte (an TEM5α polypeptide)for binding with a limited amount of anti-TEM5α antibody. The amount ofa TEM5α polypeptide in the test sample is inversely proportional to theamount of standard that becomes bound to the antibodies. To facilitatedetermining the amount of standard that becomes bound, the antibodiestypically are insolubilized before or after the competition, so that thestandard and analyte that are bound to the antibodies may convenientlybe separated from the standard and analyte that remain unbound.

Sandwich assays typically involve the use of two antibodies, eachcapable of binding to a different immunogenic portion, or epitope, ofthe protein to be detected and/or quantitated. In a sandwich assay, thetest sample analyte is typically bound by a first antibody that isimmobilized on a solid support, and thereafter a second antibody bindsto the analyte, thus forming an insoluble three-part complex. See, e.g.,U.S. Pat. No. 4,376,110. The second antibody may itself be labeled witha detectable moiety (direct sandwich assays) or may be measured using ananti-immunoglobulin antibody that is labeled with a detectable moiety(indirect sandwich assays). For example, one type of sandwich assay isan enzyme-linked immunosorbent assay (ELISA), in which case thedetectable moiety is an enzyme.

The selective binding agents, including anti-TEM5α antibodies, are alsouseful for in vivo imaging. An antibody labeled with a detectable moietymay be administered to an animal, preferably into the bloodstream, andthe presence and location of the labeled antibody in the host assayed.The antibody may be labeled with any moiety that is detectable in ananimal, whether by nuclear magnetic resonance, radiology, or otherdetection means known in the art.

Selective binding agents of the invention, including antibodies, may beused as therapeutics. These therapeutic agents are generally agonists orantagonists, in that they either enhance or reduce, respectively, atleast one of the biological activities of a TEM5α polypeptide. In oneembodiment, antagonist antibodies of the invention are antibodies orbinding fragments thereof which are capable of specifically binding to aTEM5α polypeptide and which are capable of inhibiting or eliminating thefunctional activity of a TEM5α polypeptide in vivo or in vitro. Inpreferred embodiments, the selective binding agent, e.g., an antagonistantibody, will inhibit the functional activity of a TEM5α polypeptide byat least about 50%, and preferably by at least about 80%. In anotherembodiment, the selective binding agent may be an anti-TEM5α polypeptideantibody that is capable of interacting with a TEM5α polypeptide bindingpartner (a ligand or receptor) thereby inhibiting or eliminating TEM5αpolypeptide activity in vitro or in vivo. Selective binding agents,including agonist and antagonist anti-TEM5α polypeptide antibodies, areidentified by screening assays that are well known in the art.

The invention also relates to a kit comprising TEM5α selective bindingagents (such as antibodies) and other reagents useful for detectingTEM5α polypeptide levels in biological samples. Such reagents mayinclude a detectable label, blocking serum, positive and negativecontrol samples, and detection reagents.

Microarrays

It will be appreciated that DNA microarray technology can be utilized inaccordance with the present invention. DNA microarrays are miniature,high-density arrays of nucleic acids positioned on a solid support, suchas glass. Each cell or element within the array contains numerous copiesof a single nucleic acid species that acts as a target for hybridizationwith a complementary nucleic acid sequence (e.g., mRNA). In expressionprofiling using DNA microarray technology, mRNA is first extracted froma cell or tissue sample and then converted enzymatically tofluorescently labeled cDNA. This material is hybridized to themicroarray and unbound cDNA is removed by washing. The expression ofdiscrete genes represented on the array is then visualized byquantitating the amount of labeled cDNA that is specifically bound toeach target nucleic acid molecule. In this way, the expression ofthousands of genes can be quantitated in a high throughput, parallelmanner from a single sample of biological material.

This high throughput expression profiling has a broad range ofapplications with respect to the TEM5α molecules of the invention,including, but not limited to: the identification and validation ofTEM5α disease-related genes as targets for therapeutics; moleculartoxicology of related TEM5α molecules and inhibitors thereof;stratification of populations and generation of surrogate markers forclinical trials; and enhancing related TEM5α polypeptide small moleculedrug discovery by aiding in the identification of selective compounds inhigh throughput screens.

Chemical Derivatives

Chemically modified derivatives of TEM5α polypeptides may be prepared byone skilled in the art, given the disclosures described herein. TEM5αpolypeptide derivatives are modified in a manner that isdifferent—either in the type or location of the molecules naturallyattached to the polypeptide. Derivatives may include molecules formed bythe deletion of one or more naturally-attached chemical groups. Thepolypeptide comprising the amino acid sequence of either SEQ ID NO: 2 orSEQ ID NO: 4, or other TEM5α polypeptide, may be modified by thecovalent attachment of one or more polymers. For example, the polymerselected is typically water-soluble so that the protein to which it isattached does not precipitate in an aqueous environment, such as aphysiological environment. Included within the scope of suitablepolymers is a mixture of polymers. Preferably, for therapeutic use ofthe end-product preparation, the polymer will be pharmaceuticallyacceptable.

The polymers each may be of any molecular weight and may be branched orunbranched. The polymers each typically have an average molecular weightof between about 2 kDa to about 100 kDa (the term “about” indicatingthat in preparations of a water-soluble polymer, some molecules willweigh more, some less, than the stated molecular weight). The averagemolecular weight of each polymer is preferably between about 5 kDa andabout 50 kDa, more preferably between about 12 kDa and about 40 kDa andmost preferably between about 20 kDa and about 35 kDa.

Suitable water-soluble polymers or mixtures thereof include, but are notlimited to, N-linked or O-linked carbohydrates, sugars, phosphates,polyethylene glycol (PEG) (including the forms of PEG that have beenused to derivatize proteins, including mono-(C₁-C₁₀), alkoxy-, oraryloxy-polyethylene glycol), monomethoxy-polyethylene glycol, dextran(such as low molecular weight dextran of, for example, about 6 kD),cellulose, or other carbohydrate based polymers, poly-(N-vinylpyrrolidone) polyethylene glycol, propylene glycol homopolymers,polypropylene oxide/ethylene oxide co-polymers, polyoxyethylated polyols(e.g., glycerol), and polyvinyl alcohol. Also encompassed by the presentinvention are bifunctional crosslinking molecules that may be used toprepare covalently attached TEM5α polypeptide multimers.

In general, chemical derivatization may be performed under any suitablecondition used to react a protein with an activated polymer molecule.Methods for preparing chemical derivatives of polypeptides willgenerally comprise the steps of: (a) reacting the polypeptide with theactivated polymer molecule (such as a reactive ester or aldehydederivative of the polymer molecule) under conditions whereby thepolypeptide comprising the amino acid sequence of either SEQ ID NO: 2 orSEQ ID NO: 4, or other TEM5α polypeptide, becomes attached to one ormore polymer molecules, and (b) obtaining the reaction products. Theoptimal reaction conditions will be determined based on known parametersand the desired result. For example, the larger the ratio of polymermolecules to protein, the greater the percentage of attached polymermolecule. In one embodiment, the TEM5α polypeptide derivative may have asingle polymer molecule moiety at the amino-terminus See, e.g., U.S.Pat. No. 5,234,784.

The pegylation of a polypeptide may be specifically carried out usingany of the pegylation reactions known in the art. Such reactions aredescribed, for example, in the following references: Francis et al.,1992, Focus on Growth Factors 3:4-10; European Patent Nos. 0154316 and0401384; and U.S. Pat. No. 4,179,337. For example, pegylation may becarried out via an acylation reaction or an alkylation reaction with areactive polyethylene glycol molecule (or an analogous reactivewater-soluble polymer) as described herein. For the acylation reactions,a selected polymer should have a single reactive ester group. Forreductive alkylation, a selected polymer should have a single reactivealdehyde group. A reactive aldehyde is, for example, polyethylene glycolpropionaldehyde, which is water stable, or mono C₁-C₁₀ alkoxy or aryloxyderivatives thereof (see U.S. Pat. No. 5,252,714).

In another embodiment, TEM5α polypeptides may be chemically coupled tobiotin. The biotin/TEM5α polypeptide molecules are then allowed to bindto avidin, resulting in tetravalent avidin/biotin/TEM5α polypeptidemolecules. TEM5α polypeptides may also be covalently coupled todinitrophenol (DNP) or trinitrophenol (TNP) and the resulting conjugatesprecipitated with anti-DNP or anti-TNP-IgM to form decameric conjugateswith a valency of 10.

Generally, conditions that may be alleviated or modulated by theadministration of the present TEM5α polypeptide derivatives includethose described herein for TEM5α polypeptides. However, the TEM5αpolypeptide derivatives disclosed herein may have additional activities,enhanced or reduced biological activity, or other characteristics, suchas increased or decreased half-life, as compared to the non-derivatizedmolecules.

Genetically Engineered Non-Human Animals

Additionally included within the scope of the present invention arenon-human animals such as mice, rats, or other rodents; rabbits, goats,sheep, or other farm animals, in which the genes encoding native TEM5αpolypeptide have been disrupted (i.e., “knocked out”) such that thelevel of expression of TEM5α polypeptide is significantly decreased orcompletely abolished. Such animals may be prepared using techniques andmethods such as those described in U.S. Pat. No. 5,557,032.

The present invention further includes non-human animals such as mice,rats, or other rodents; rabbits, goats, sheep, or other farm animals, inwhich either the native form of a TEM5α gene for that animal or aheterologous TEM5α gene is over-expressed by the animal, therebycreating a “transgenic” animal. Such transgenic animals may be preparedusing well known methods such as those described in U.S. Pat. No.5,489,743 and International Pub. No. WO 94/28122.

The present invention further includes non-human animals in which thepromoter for one or more of the TEM5α polypeptides of the presentinvention is either activated or inactivated (e.g., by using homologousrecombination methods) to alter the level of expression of one or moreof the native TEM5α polypeptides.

These non-human animals may be used for drug candidate screening. Insuch screening, the impact of a drug candidate on the animal may bemeasured. For example, drug candidates may decrease or increase theexpression of the TEM5α gene. In certain embodiments, the amount ofTEM5α polypeptide that is produced may be measured after the exposure ofthe animal to the drug candidate. Additionally, in certain embodiments,one may detect the actual impact of the drug candidate on the animal.For example, over-expression of a particular gene may result in, or beassociated with, a disease or pathological condition. In such cases, onemay test a drug candidate's ability to decrease expression of the geneor its ability to prevent or inhibit a pathological condition. In otherexamples, the production of a particular metabolic product such as afragment of a polypeptide, may result in, or be associated with, adisease or pathological condition. In such cases, one may test a drugcandidate's ability to decrease the production of such a metabolicproduct or its ability to prevent or inhibit a pathological condition.

Assaying for Other Modulators of TEM5α Polypeptide Activity

In some situations, it may be desirable to identify molecules that aremodulators, i.e., agonists or antagonists, of the activity of TEM5αpolypeptide. Natural or synthetic molecules that modulate TEM5αpolypeptide may be identified using one or more screening assays, suchas those described herein. Such molecules may be administered either inan ex vivo manner or in an in vivo manner by injection, or by oraldelivery, implantation device, or the like.

“Test molecule” refers to a molecule that is under evaluation for theability to modulate (i.e., increase or decrease) the activity of a TEM5αpolypeptide. Most commonly, a test molecule will interact directly witha TEM5α polypeptide. However, it is also contemplated that a testmolecule may also modulate TEM5α polypeptide activity indirectly, suchas by affecting TEM5α gene expression, or by binding to a TEM5αpolypeptide binding partner (e.g., receptor or ligand). In oneembodiment, a test molecule will bind to a TEM5α polypeptide with anaffinity constant of at least about 10⁻⁶ M, preferably about 10⁻⁸ M,more preferably about 10⁻⁹ M, and even more preferably about 10⁻¹⁰ M.

Methods for identifying compounds that interact with TEM5α polypeptidesare encompassed by the present invention. In certain embodiments, aTEM5α polypeptide is incubated with a test molecule under conditionsthat permit the interaction of the test molecule with a TEM5αpolypeptide, and the extent of the interaction is measured. The testmolecule can be screened in a substantially purified form or in a crudemixture.

In certain embodiments, a TEM5α polypeptide agonist or antagonist may bea protein, peptide, carbohydrate, lipid, or small molecular weightmolecule that interacts with TEM5α polypeptide to regulate its activity.Molecules which regulate TEM5α polypeptide expression include nucleicacids which are complementary to nucleic acids encoding a TEM5αpolypeptide, or are complementary to nucleic acids sequences whichdirect or control the expression of TEM5α polypeptide, and which act asanti-sense regulators of expression.

Once a test molecule has been identified as interacting with a TEM5αpolypeptide, the molecule may be further evaluated for its ability toincrease or decrease TEM5α polypeptide activity. The measurement of theinteraction of a test molecule with TEM5α polypeptide may be carried outin several formats, including cell-based binding assays, membranebinding assays, solution-phase assays, and immunoassays. In general, atest molecule is incubated with a TEM5α polypeptide for a specifiedperiod of time, and TEM5α polypeptide activity is determined by one ormore assays for measuring biological activity.

The interaction of test molecules with TEM5α polypeptides may also beassayed directly using polyclonal or monoclonal antibodies in animmunoassay. Alternatively, modified forms of TEM5α polypeptidescontaining epitope tags as described herein may be used in solution andimmunoassays.

In the event that TEM5α polypeptides display biological activity throughan interaction with a binding partner (e.g., a receptor or a ligand), avariety of in vitro assays may be used to measure the binding of a TEM5αpolypeptide to the corresponding binding partner (such as a selectivebinding agent, receptor, or ligand). These assays may be used to screentest molecules for their ability to increase or decrease the rate and/orthe extent of binding of a TEM5α polypeptide to its binding partner. Inone assay, a TEM5α polypeptide is immobilized in the wells of amicrotiter plate. Radiolabeled TEM5α polypeptide binding partner (forexample, iodinated TEM5α polypeptide binding partner) and a testmolecule can then be added either one at a time (in either order) orsimultaneously to the wells. After incubation, the wells can be washedand counted for radioactivity, using a scintillation counter, todetermine the extent to which the binding partner bound to the TEM5αpolypeptide. Typically, a molecule will be tested over a range ofconcentrations, and a series of control wells lacking one or moreelements of the test assays can be used for accuracy in the evaluationof the results. An alternative to this method involves reversing the“positions” of the proteins, i.e., immobilizing TEM5α polypeptidebinding partner to the microtiter plate wells, incubating with the testmolecule and radiolabeled TEM5α polypeptide, and determining the extentof TEM5α polypeptide binding. See, e.g., Current Protocols in MolecularBiology, chap. 18 (Ausubel et al., eds., Green Publishers Inc. and Wileyand Sons 1995).

As an alternative to radiolabeling, a TEM5α polypeptide or its bindingpartner may be conjugated to biotin, and the presence of biotinylatedprotein can then be detected using streptavidin linked to an enzyme,such as horse radish peroxidase (HRP) or alkaline phosphatase (AP),which can be detected colorometrically, or by fluorescent tagging ofstreptavidin. An antibody directed to a TEM5α polypeptide or to a TEM5αpolypeptide binding partner, and which is conjugated to biotin, may alsobe used for purposes of detection following incubation of the complexwith enzyme-linked streptavidin linked to AP or HRP.

A TEM5α polypeptide or a TEM5α polypeptide binding partner can also beimmobilized by attachment to agarose beads, acrylic beads, or othertypes of such inert solid phase substrates. The substrate-proteincomplex can be placed in a solution containing the complementary proteinand the test compound. After incubation, the beads can be precipitatedby centrifugation, and the amount of binding between a TEM5α polypeptideand its binding partner can be assessed using the methods describedherein. Alternatively, the substrate-protein complex can be immobilizedin a column with the test molecule and complementary protein passingthrough the column. The formation of a complex between a TEM5αpolypeptide and its binding partner can then be assessed using any ofthe techniques described herein (e.g., radiolabelling or antibodybinding).

Another in vitro assay that is useful for identifying a test moleculethat increases or decreases the formation of a complex between a TEM5αpolypeptide binding protein and a TEM5α polypeptide binding partner is asurface plasmon resonance detector system such as the BIAcore assaysystem (Pharmacia, Piscataway, N.J.). The BIAcore system is utilized asspecified by the manufacturer. This assay essentially involves thecovalent binding of either TEM5α polypeptide or a TEM5α polypeptidebinding partner to a dextran-coated sensor chip that is located in adetector. The test compound and the other complementary protein can thenbe injected, either simultaneously or sequentially, into the chambercontaining the sensor chip. The amount of complementary protein thatbinds can be assessed based on the change in molecular mass that isphysically associated with the dextran-coated side of the sensor chip,with the change in molecular mass being measured by the detector system.

In some cases, it may be desirable to evaluate two or more testcompounds together for their ability to increase or decrease theformation of a complex between a TEM5α polypeptide and a TEM5αpolypeptide binding partner. In these cases, the assays set forth hereincan be readily modified by adding such additional test compound(s)either simultaneously with, or subsequent to, the first test compound.The remainder of the steps in the assay are as set forth herein.

In vitro assays such as those described herein may be usedadvantageously to screen large numbers of compounds for an effect on theformation of a complex between a TEM5α polypeptide and TEM5α polypeptidebinding partner. The assays may be automated to screen compoundsgenerated in phage display, synthetic peptide, and chemical synthesislibraries.

Compounds which increase or decrease the formation of a complex betweena TEM5α polypeptide and a TEM5α polypeptide binding partner may also bescreened in cell culture using cells and cell lines expressing eitherTEM5α polypeptide or TEM5α polypeptide binding partner. Cells and celllines may be obtained from any mammal, but preferably will be from humanor other primate, canine, or rodent sources. The binding of a TEM5αpolypeptide to cells expressing TEM5α polypeptide binding partner at thesurface is evaluated in the presence or absence of test molecules, andthe extent of binding may be determined by, for example, flow cytometryusing a biotinylated antibody to a TEM5α polypeptide binding partner.Cell culture assays can be used advantageously to further evaluatecompounds that score positive in protein binding assays describedherein.

Cell cultures can also be used to screen the impact of a drug candidate.For example, drug candidates may decrease or increase the expression ofthe TEM5α gene. In certain embodiments, the amount of TEM5α polypeptideor a TEM5α polypeptide fragment that is produced may be measured afterexposure of the cell culture to the drug candidate. In certainembodiments, one may detect the actual impact of the drug candidate onthe cell culture. For example, the over-expression of a particular genemay have a particular impact on the cell culture. In such cases, one maytest a drug candidate's ability to increase or decrease the expressionof the gene or its ability to prevent or inhibit a particular impact onthe cell culture. In other examples, the production of a particularmetabolic product such as a fragment of a polypeptide, may result in, orbe associated with, a disease or pathological condition. In such cases,one may test a drug candidate's ability to decrease the production ofsuch a metabolic product in a cell culture.

Internalizing Proteins

The tat at protein sequence (from HIV) can be used to internalizeproteins into a cell. See, e.g., Falwell et al., 1994, Proc. Natl. Acad.Sci. U.S.A. 91:664-68. For example, an 11 amino acid sequence(Y-G-R-K-K-R-R-Q-R-R-R; SEQ ID NO: 6) of the HIV tat protein (termed the“protein transduction domain,” or TAT PDT) has been described asmediating delivery across the cytoplasmic membrane and the nuclearmembrane of a cell. See Schwarze et al., 1999, Science 285:1569-72; andNagahara et al., 1998, Nat. Med. 4:1449-52. In these procedures,FITC-constructs (FITC-labeled G-G-G-G-Y-G-R-K-K-R-R-Q-R-R-R; SEQ ID NO:7), which penetrate tissues following intraperitoneal administration,are prepared, and the binding of such constructs to cells is detected byfluorescence-activated cell sorting (FACS) analysis. Cells treated witha tat-β-gal fusion protein will demonstrate β-gal activity. Followinginjection, expression of such a construct can be detected in a number oftissues, including liver, kidney, lung, heart, and brain tissue. It isbelieved that such constructs undergo some degree of unfolding in orderto enter the cell, and as such, may require a refolding following entryinto the cell.

It will thus be appreciated that the tat protein sequence may be used tointernalize a desired polypeptide into a cell. For example, using thetat protein sequence, a TEM5α antagonist (such as an anti-TEM5αselective binding agent, small molecule, soluble receptor, or antisenseoligonucleotide) can be administered intracellularly to inhibit theactivity of a TEM5α molecule. As used herein, the term “TEM5α molecule”refers to both TEM5α nucleic acid molecules and TEM5α polypeptides asdefined herein. Where desired, the TEM5α protein itself may also beinternally administered to a cell using these procedures. See also,Straus, 1999, Science 285:1466-67.

Cell Source Identification Using TEM5α Polypeptide

In accordance with certain embodiments of the invention, it may beuseful to be able to determine the source of a certain cell typeassociated with a TEM5α polypeptide. For example, it may be useful todetermine the origin of a disease or pathological condition as an aid inselecting an appropriate therapy. In certain embodiments, nucleic acidsencoding a TEM5α polypeptide can be used as a probe to identify cellsdescribed herein by screening the nucleic acids of the cells with such aprobe. In other embodiments, one may use anti-TEM5α polypeptideantibodies to test for the presence of TEM5α polypeptide in cells, andthus, determine if such cells are of the types described herein.

TEM5α Polypeptide Compositions and Administration

Therapeutic compositions are within the scope of the present invention.Such TEM5α polypeptide pharmaceutical compositions may comprise atherapeutically effective amount of a TEM5α polypeptide or a TEM5αnucleic acid molecule in admixture with a pharmaceutically orphysiologically acceptable formulation agent selected for suitabilitywith the mode of administration. Pharmaceutical compositions maycomprise a therapeutically effective amount of one or more TEM5αpolypeptide selective binding agents in admixture with apharmaceutically or physiologically acceptable formulation agentselected for suitability with the mode of administration.

Acceptable formulation materials preferably are nontoxic to recipientsat the dosages and concentrations employed.

The pharmaceutical composition may contain formulation materials formodifying, maintaining, or preserving, for example, the pH, osmolarity,viscosity, clarity, color, isotonicity, odor, sterility, stability, rateof dissolution or release, adsorption, or penetration of thecomposition. Suitable formulation materials include, but are not limitedto, amino acids (such as glycine, glutamine, asparagine, arginine, orlysine), antimicrobials, antioxidants (such as ascorbic acid, sodiumsulfite, or sodium hydrogen-sulfite), buffers (such as borate,bicarbonate, Tris-HCl, citrates, phosphates, or other organic acids),bulking agents (such as mannitol or glycine), chelating agents (such asethylenediamine tetraacetic acid (EDTA)), complexing agents (such ascaffeine, polyvinylpyrrolidone, beta-cyclodextrin, orhydroxypropyl-beta-cyclodextrin), fillers, monosaccharides,disaccharides, and other carbohydrates (such as glucose, mannose, ordextrins), proteins (such as serum albumin, gelatin, orimmunoglobulins), coloring, flavoring and diluting agents, emulsifyingagents, hydrophilic polymers (such as polyvinylpyrrolidone), lowmolecular weight polypeptides, salt-forming counterions (such assodium), preservatives (such as benzalkonium chloride, benzoic acid,salicylic acid, thimerosal, phenethyl alcohol, methylparaben,propylparaben, chlorhexidine, sorbic acid, or hydrogen peroxide),solvents (such as glycerin, propylene glycol, or polyethylene glycol),sugar alcohols (such as mannitol or sorbitol), suspending agents,surfactants or wetting agents (such as pluronics; PEG; sorbitan esters;polysorbates such as polysorbate 20 or polysorbate 80; triton;tromethamine; lecithin; cholesterol or tyloxapal), stability enhancingagents (such as sucrose or sorbitol), tonicity enhancing agents (such asalkali metal halides—preferably sodium or potassium chloride—or mannitolsorbitol), delivery vehicles, diluents, excipients and/or pharmaceuticaladjuvants. See Remington's Pharmaceutical Sciences (18th Ed., A. R.Gennaro, ed., Mack Publishing Company 1990.

The optimal pharmaceutical composition will be determined by a skilledartisan depending upon, for example, the intended route ofadministration, delivery format, and desired dosage. See, e.g.,Remington's Pharmaceutical Sciences, supra. Such compositions mayinfluence the physical state, stability, rate of in vivo release, andrate of in vivo clearance of the TEM5α molecule.

The primary vehicle or carrier in a pharmaceutical composition may beeither aqueous or non-aqueous in nature. For example, a suitable vehicleor carrier for injection may be water, physiological saline solution, orartificial cerebrospinal fluid, possibly supplemented with othermaterials common in compositions for parenteral administration. Neutralbuffered saline or saline mixed with serum albumin are further exemplaryvehicles. Other exemplary pharmaceutical compositions comprise Trisbuffer of about pH 7.0-8.5, or acetate buffer of about pH 4.0-5.5, whichmay further include sorbitol or a suitable substitute. In one embodimentof the present invention, TEM5α polypeptide compositions may be preparedfor storage by mixing the selected composition having the desired degreeof purity with optional formulation agents (Remington's PharmaceuticalSciences, supra) in the form of a lyophilized cake or an aqueoussolution. Further, the TEM5α polypeptide product may be formulated as alyophilizate using appropriate excipients such as sucrose.

The TEM5α polypeptide pharmaceutical compositions can be selected forparenteral delivery. Alternatively, the compositions may be selected forinhalation or for delivery through the digestive tract, such as orally.The preparation of such pharmaceutically acceptable compositions iswithin the skill of the art.

The formulation components are present in concentrations that areacceptable to the site of administration. For example, buffers are usedto maintain the composition at physiological pH or at a slightly lowerpH, typically within a pH range of from about 5 to about 8.

When parenteral administration is contemplated, the therapeuticcompositions for use in this invention may be in the form of apyrogen-free, parenterally acceptable, aqueous solution comprising thedesired TEM5α molecule in a pharmaceutically acceptable vehicle. Aparticularly suitable vehicle for parenteral injection is steriledistilled water in which a TEM5α molecule is formulated as a sterile,isotonic solution, properly preserved. Yet another preparation caninvolve the formulation of the desired molecule with an agent, such asinjectable microspheres, bio-erodible particles, polymeric compounds(such as polylactic acid or polyglycolic acid), beads, or liposomes,that provides for the controlled or sustained release of the productwhich may then be delivered via a depot injection. Hyaluronic acid mayalso be used, and this may have the effect of promoting sustainedduration in the circulation. Other suitable means for the introductionof the desired molecule include implantable drug delivery devices.

In one embodiment, a pharmaceutical composition may be formulated forinhalation. For example, TEM5α polypeptide may be formulated as a drypowder for inhalation. TEM5α polypeptide or nucleic acid moleculeinhalation solutions may also be formulated with a propellant foraerosol delivery. In yet another embodiment, solutions may be nebulized.Pulmonary administration is further described in International Pub. No.WO 94/20069, which describes the pulmonary delivery of chemicallymodified proteins.

It is also contemplated that certain formulations may be administeredorally. In one embodiment of the present invention, TEM5α polypeptidesthat are administered in this fashion can be formulated with or withoutthose carriers customarily used in the compounding of solid dosage formssuch as tablets and capsules. For example, a capsule may be designed torelease the active portion of the formulation at the point in thegastrointestinal tract when bioavailability is maximized andpre-systemic degradation is minimized. Additional agents can be includedto facilitate absorption of the TEM5α polypeptide. Diluents, flavorings,low melting point waxes, vegetable oils, lubricants, suspending agents,tablet disintegrating agents, and binders may also be employed.

Another pharmaceutical composition may involve an effective quantity ofTEM5α polypeptides in a mixture with non-toxic excipients that aresuitable for the manufacture of tablets. By dissolving the tablets insterile water, or another appropriate vehicle, solutions can be preparedin unit-dose form. Suitable excipients include, but are not limited to,inert diluents, such as calcium carbonate, sodium carbonate orbicarbonate, lactose, or calcium phosphate; or binding agents, such asstarch, gelatin, or acacia; or lubricating agents such as magnesiumstearate, stearic acid, or talc.

Additional TEM5α polypeptide pharmaceutical compositions will be evidentto those skilled in the art, including formulations involving TEM5αpolypeptides in sustained- or controlled-delivery formulations.Techniques for formulating a variety of other sustained- orcontrolled-delivery means, such as liposome carriers, bio-erodiblemicroparticles or porous beads and depot injections, are also known tothose skilled in the art. See, e.g., International Pub. No. WO 93/15722,which describes the controlled release of porous polymericmicroparticles for the delivery of pharmaceutical compositions.

Additional examples of sustained-release preparations includesemipermeable polymer matrices in the form of shaped articles, e.g.films, or microcapsules. Sustained release matrices may includepolyesters, hydrogels, polylactides (U.S. Pat. No. 3,773,919 andEuropean Patent No. 058481), copolymers of L-glutamic acid and gammaethyl-L-glutamate (Sidman et al., 1983, Biopolymers 22:547-56),poly(2-hydroxyethyl-methacrylate) (Langer et al., 1981, J. Biomed.Mater. Res. 15:167-277 and Langer, 1982, Chem. Tech. 12:98-105),ethylene vinyl acetate (Langer et al., supra) orpoly-D(−)-3-hydroxybutyric acid (European Patent No. 133988).Sustained-release compositions may also include liposomes, which can beprepared by any of several methods known in the art. See, e.g., Eppsteinet al., 1985, Proc. Natl. Acad. Sci. USA 82:3688-92; and European PatentNos. 036676, 088046, and 143949.

The TEM5α pharmaceutical composition to be used for in vivoadministration typically must be sterile. This may be accomplished byfiltration through sterile filtration membranes. Where the compositionis lyophilized, sterilization using this method may be conducted eitherprior to, or following, lyophilization and reconstitution. Thecomposition for parenteral administration may be stored in lyophilizedform or in a solution. In addition, parenteral compositions generallyare placed into a container having a sterile access port, for example,an intravenous solution bag or vial having a stopper pierceable by ahypodermic injection needle.

Once the pharmaceutical composition has been formulated, it may bestored in sterile vials as a solution, suspension, gel, emulsion, solid,or as a dehydrated or lyophilized powder. Such formulations may bestored either in a ready-to-use form or in a form (e.g., lyophilized)requiring reconstitution prior to administration.

In a specific embodiment, the present invention is directed to kits forproducing a single-dose administration unit. The kits may each containboth a first container having a dried protein and a second containerhaving an aqueous formulation. Also included within the scope of thisinvention are kits containing single and multi-chambered pre-filledsyringes (e.g., liquid syringes and lyosyringes).

The effective amount of a TEM5α pharmaceutical composition to beemployed therapeutically will depend, for example, upon the therapeuticcontext and objectives. One skilled in the art will appreciate that theappropriate dosage levels for treatment will thus vary depending, inpart, upon the molecule delivered, the indication for which the TEM5αmolecule is being used, the route of administration, and the size (bodyweight, body surface, or organ size) and condition (the age and generalhealth) of the patient. Accordingly, the clinician may titer the dosageand modify the route of administration to obtain the optimal therapeuticeffect. A typical dosage may range from about 0.1 μg/kg to up to about100 mg/kg or more, depending on the factors mentioned above. In otherembodiments, the dosage may range from 0.1 μg/kg up to about 100 mg/kg;or 1 μg/kg up to about 100 mg/kg; or 5 μg/kg up to about 100 mg/kg.

The frequency of dosing will depend upon the pharmacokinetic parametersof the TEM5α molecule in the formulation being used. Typically, aclinician will administer the composition until a dosage is reached thatachieves the desired effect. The composition may therefore beadministered as a single dose, as two or more doses (which may or maynot contain the same amount of the desired molecule) over time, or as acontinuous infusion via an implantation device or catheter. Furtherrefinement of the appropriate dosage is routinely made by those ofordinary skill in the art and is within the ambit of tasks routinelyperformed by them. Appropriate dosages may be ascertained through use ofappropriate dose-response data.

The route of administration of the pharmaceutical composition is inaccord with known methods, e.g., orally; through injection byintravenous, intraperitoneal, intracerebral (intraparenchymal),intracerebroventricular, intramuscular, intraocular, intraarterial,intraportal, or intralesional routes; by sustained release systems; orby implantation devices. Where desired, the compositions may beadministered by bolus injection or continuously by infusion, or byimplantation device.

Alternatively or additionally, the composition may be administeredlocally via implantation of a membrane, sponge, or other appropriatematerial onto which the desired molecule has been absorbed orencapsulated. Where an implantation device is used, the device may beimplanted into any suitable tissue or organ, and delivery of the desiredmolecule may be via diffusion, timed-release bolus, or continuousadministration.

In some cases, it may be desirable to use TEM5α polypeptidepharmaceutical compositions in an ex vivo manner. In such instances,cells, tissues, or organs that have been removed from the patient areexposed to TEM5α polypeptide pharmaceutical compositions after which thecells, tissues, or organs are subsequently implanted back into thepatient.

In other cases, a TEM5α polypeptide can be delivered by implantingcertain cells that have been genetically engineered, using methods suchas those described herein, to express and secrete the TEM5α polypeptide.Such cells may be animal or human cells, and may be autologous,heterologous, or xenogeneic. Optionally, the cells may be immortalized.In order to decrease the chance of an immunological response, the cellsmay be encapsulated to avoid infiltration of surrounding tissues. Theencapsulation materials are typically biocompatible, semi-permeablepolymeric enclosures or membranes that allow the release of the proteinproduct(s) but prevent the destruction of the cells by the patient'simmune system or by other detrimental factors from the surroundingtissues.

As discussed herein, it may be desirable to treat isolated cellpopulations (such as stem cells, lymphocytes, red blood cells,chondrocytes, neurons, and the like) with one or more TEM5αpolypeptides. This can be accomplished by exposing the isolated cells tothe polypeptide directly, where it is in a form that is permeable to thecell membrane.

Additional embodiments of the present invention relate to cells andmethods (e.g., homologous recombination and/or other recombinantproduction methods) for both the in vitro production of therapeuticpolypeptides and for the production and delivery of therapeuticpolypeptides by gene therapy or cell therapy. Homologous and otherrecombination methods may be used to modify a cell that contains anormally transcriptionally-silent TEM5α gene, or an under-expressedgene, and thereby produce a cell which expresses therapeuticallyefficacious amounts of TEM5α polypeptides.

Homologous recombination is a technique originally developed fortargeting genes to induce or correct mutations in transcriptionallyactive genes. Kucherlapati, 1989, Prog. in Nucl. Acid Res. & Mol. Biol.36:301. The basic technique was developed as a method for introducingspecific mutations into specific regions of the mammalian genome (Thomaset al., 1986, Cell 44:419-28; Thomas and Capecchi, 1987, Cell 51:503-12;Doetschman et al., 1988, Proc. Natl. Acad. Sci. U.S.A. 85:8583-87) or tocorrect specific mutations within defective genes (Doetschman et al.,1987, Nature 330:576-78). Exemplary homologous recombination techniquesare described in U.S. Pat. No. 5,272,071; European Patent Nos. 9193051and 505500; and International Pub. Nos. WO 91/09955 and WO 91/09955).

Through homologous recombination, the DNA sequence to be inserted intothe genome can be directed to a specific region of the gene of interestby attaching it to targeting DNA. The targeting DNA is a nucleotidesequence that is complementary (homologous) to a region of the genomicDNA. Small pieces of targeting DNA that are complementary to a specificregion of the genome are put in contact with the parental strand duringthe DNA replication process. It is a general property of DNA that hasbeen inserted into a cell to hybridize, and therefore, recombine withother pieces of endogenous DNA through shared homologous regions. Ifthis complementary strand is attached to an oligonucleotide thatcontains a mutation or a different sequence or an additional nucleotide,it too is incorporated into the newly synthesized strand as a result ofthe recombination. As a result of the proofreading function, it ispossible for the new sequence of DNA to serve as the template. Thus, thetransferred DNA is incorporated into the genome.

Attached to these pieces of targeting DNA are regions of DNA that mayinteract with or control the expression of a TEM5α polypeptide, e.g.,flanking sequences. For example, a promoter/enhancer element, asuppressor, or an exogenous transcription modulatory element is insertedin the genome of the intended host cell in proximity and orientationsufficient to influence the transcription of DNA encoding the desiredTEM5α polypeptide. The control element controls a portion of the DNApresent in the host cell genome. Thus, the expression of the desiredTEM5α polypeptide may be achieved not by transfection of DNA thatencodes the TEM5α gene itself, but rather by the use of targeting DNA(containing regions of homology with the endogenous gene of interest)coupled with DNA regulatory segments that provide the endogenous genesequence with recognizable signals for transcription of a TEM5α gene.

In an exemplary method, the expression of a desired targeted gene in acell (i.e., a desired endogenous cellular gene) is altered viahomologous recombination into the cellular genome at a preselected site,by the introduction of DNA that includes at least a regulatory sequence,an exon, and a splice donor site. These components are introduced intothe chromosomal (genomic) DNA in such a manner that this, in effect,results in the production of a new transcription unit (in which theregulatory sequence, the exon, and the splice donor site present in theDNA construct are operatively linked to the endogenous gene). As aresult of the introduction of these components into the chromosomal DNA,the expression of the desired endogenous gene is altered.

Altered gene expression, as described herein, encompasses activating (orcausing to be expressed) a gene which is normally silent (unexpressed)in the cell as obtained, as well as increasing the expression of a genewhich is not expressed at physiologically significant levels in the cellas obtained. The embodiments further encompass changing the pattern ofregulation or induction such that it is different from the pattern ofregulation or induction that occurs in the cell as obtained, andreducing (including eliminating) the expression of a gene which isexpressed in the cell as obtained.

One method by which homologous recombination can be used to increase, orcause, TEM5α polypeptide production from a cell's endogenous TEM5α geneinvolves first using homologous recombination to place a recombinationsequence from a site-specific recombination system (e.g., Cre/loxP,FLP/FRT) (Sauer, 1994, Curr. Opin. Biotechnol., 5:521-27; Sauer, 1993,Methods Enzymol., 225:890-900) upstream of (i.e., 5′ to) the cell'sendogenous genomic TEM5α polypeptide coding region. A plasmid containinga recombination site homologous to the site that was placed justupstream of the genomic TEM5α polypeptide coding region is introducedinto the modified cell line along with the appropriate recombinaseenzyme. This recombinase causes the plasmid to integrate, via theplasmid's recombination site, into the recombination site located justupstream of the genomic TEM5α polypeptide coding region in the cell line(Baubonis and Sauer, 1993, Nucleic Acids Res. 21:2025-29; O'Gorman etal., 1991, Science 251:1351-55). Any flanking sequences known toincrease transcription (e.g., enhancer/promoter, intron, translationalenhancer), if properly positioned in this plasmid, would integrate insuch a manner as to create a new or modified transcriptional unitresulting in de novo or increased TEM5α polypeptide production from thecell's endogenous TEM5α gene.

A further method to use the cell line in which the site specificrecombination sequence had been placed just upstream of the cell'sendogenous genomic TEM5α polypeptide coding region is to use homologousrecombination to introduce a second recombination site elsewhere in thecell line's genome. The appropriate recombinase enzyme is thenintroduced into the two-recombination-site cell line, causing arecombination event (deletion, inversion, and translocation) (Sauer,1994, Curr. Opin. Biotechnol., 5:521-27; Sauer, 1993, Methods Enzymol.,225:890-900) that would create a new or modified transcriptional unitresulting in de novo or increased TEM5α polypeptide production from thecell's endogenous TEM5α gene.

An additional approach for increasing, or causing, the expression ofTEM5α polypeptide from a cell's endogenous TEM5α gene involvesincreasing, or causing, the expression of a gene or genes (e.g.,transcription factors) and/or decreasing the expression of a gene orgenes (e.g., transcriptional repressors) in a manner which results in denovo or increased TEM5α polypeptide production from the cell'sendogenous TEM5α gene. This method includes the introduction of anon-naturally occurring polypeptide (e.g., a polypeptide comprising asite specific DNA binding domain fused to a transcriptional factordomain) into the cell such that de novo or increased TEM5α polypeptideproduction from the cell's endogenous TEM5α gene results.

The present invention further relates to DNA constructs useful in themethod of altering expression of a target gene. In certain embodiments,the exemplary DNA constructs comprise: (a) one or more targetingsequences, (b) a regulatory sequence, (c) an exon, and (d) an unpairedsplice-donor site. The targeting sequence in the DNA construct directsthe integration of elements (a)-(d) into a target gene in a cell suchthat the elements (b)-(d) are operatively linked to sequences of theendogenous target gene. In another embodiment, the DNA constructscomprise: (a) one or more targeting sequences, (b) a regulatorysequence, (c) an exon, (d) a splice-donor site, (e) an intron, and (f) asplice-acceptor site, wherein the targeting sequence directs theintegration of elements (a)-(f) such that the elements of (b)-(f) areoperatively linked to the endogenous gene. The targeting sequence ishomologous to the preselected site in the cellular chromosomal DNA withwhich homologous recombination is to occur. In the construct, the exonis generally 3′ of the regulatory sequence and the splice-donor site is3′ of the exon.

If the sequence of a particular gene is known, such as the nucleic acidsequence of TEM5α polypeptide presented herein, a piece of DNA that iscomplementary to a selected region of the gene can be synthesized orotherwise obtained, such as by appropriate restriction of the native DNAat specific recognition sites bounding the region of interest. Thispiece serves as a targeting sequence upon insertion into the cell andwill hybridize to its homologous region within the genome. If thishybridization occurs during DNA replication, this piece of DNA, and anyadditional sequence attached thereto, will act as an Okazaki fragmentand will be incorporated into the newly synthesized daughter strand ofDNA. The present invention, therefore, includes nucleotides encoding aTEM5α polypeptide, which nucleotides may be used as targeting sequences.

TEM5α polypeptide cell therapy, e.g., the implantation of cellsproducing TEM5α polypeptides, is also contemplated. This embodimentinvolves implanting cells capable of synthesizing and secreting abiologically active form of TEM5α polypeptide. Such TEM5αpolypeptide-producing cells can be cells that are natural producers ofTEM5α polypeptides or may be recombinant cells whose ability to produceTEM5α polypeptides has been augmented by transformation with a geneencoding the desired TEM5α polypeptide or with a gene augmenting theexpression of TEM5α polypeptide. Such a modification may be accomplishedby means of a vector suitable for delivering the gene as well aspromoting its expression and secretion. In order to minimize a potentialimmunological reaction in patients being administered a TEM5αpolypeptide, as may occur with the administration of a polypeptide of aforeign species, it is preferred that the natural cells producing TEM5αpolypeptide be of human origin and produce human TEM5α polypeptide.Likewise, it is preferred that the recombinant cells producing TEM5αpolypeptide be transformed with an expression vector containing a geneencoding a human TEM5α polypeptide.

Implanted cells may be encapsulated to avoid the infiltration ofsurrounding tissue. Human or non-human animal cells may be implanted inpatients in biocompatible, semipermeable polymeric enclosures ormembranes that allow the release of TEM5α polypeptide, but that preventthe destruction of the cells by the patient's immune system or by otherdetrimental factors from the surrounding tissue. Alternatively, thepatient's own cells, transformed to produce TEM5α polypeptides ex vivo,may be implanted directly into the patient without such encapsulation.

Techniques for the encapsulation of living cells are known in the art,and the preparation of the encapsulated cells and their implantation inpatients may be routinely accomplished. For example, Baetge et al.(International Pub. No. WO 95/05452 and International Pub. No. WO95/05452) describe membrane capsules containing genetically engineeredcells for the effective delivery of biologically active molecules. Thecapsules are biocompatible and are easily retrievable. The capsulesencapsulate cells transfected with recombinant DNA molecules comprisingDNA sequences coding for biologically active molecules operativelylinked to promoters that are not subject to down-regulation in vivo uponimplantation into a mammalian host. The devices provide for the deliveryof the molecules from living cells to specific sites within a recipient.In addition, see U.S. Pat. Nos. 4,892,538; 5,011,472; and 5,106,627. Asystem for encapsulating living cells is described in International Pub.No. WO 91/10425 (Aebischer et al.). See also, International Pub. No. WO91/10470 (Aebischer et al.); Winn et al., 1991, Exper. Neurol.113:322-29; Aebischer et al., 1991, Exper. Neurol. 111:269-75; andTresco et al., 1992, ASAIO 38:17-23.

In vivo and in vitro gene therapy delivery of TEM5α polypeptides is alsoenvisioned. One example of a gene therapy technique is to use the TEM5αgene (either genomic DNA, cDNA, and/or synthetic DNA) encoding a TEM5αpolypeptide that may be operably linked to a constitutive or induciblepromoter to form a “gene therapy DNA construct.” The promoter may behomologous or heterologous to the endogenous TEM5α gene, provided thatit is active in the cell or tissue type into which the construct will beinserted. Other components of the gene therapy DNA construct mayoptionally include DNA molecules designed for site-specific integration(e.g., endogenous sequences useful for homologous recombination),tissue-specific promoters, enhancers or silencers, DNA molecules capableof providing a selective advantage over the parent cell, DNA moleculesuseful as labels to identify transformed cells, negative selectionsystems, cell specific binding agents (as, for example, for celltargeting), cell-specific internalization factors, transcription factorsenhancing expression from a vector, and factors enabling vectorproduction.

A gene therapy DNA construct can then be introduced into cells (eitherex vivo or in vivo) using viral or non-viral vectors. One means forintroducing the gene therapy DNA construct is by means of viral vectorsas described herein. Certain vectors, such as retroviral vectors, willdeliver the DNA construct to the chromosomal DNA of the cells, and thegene can integrate into the chromosomal DNA. Other vectors will functionas episomes, and the gene therapy DNA construct will remain in thecytoplasm.

In yet other embodiments, regulatory elements can be included for thecontrolled expression of the TEM5α gene in the target cell. Suchelements are turned on in response to an appropriate effector. In thisway, a therapeutic polypeptide can be expressed when desired. Oneconventional control means involves the use of small molecule dimerizersor rapalogs to dimerize chimeric proteins which contain a smallmolecule-binding domain and a domain capable of initiating a biologicalprocess, such as a DNA-binding protein or transcriptional activationprotein (see International Pub. Nos. WO 96/41865, WO 97/31898, and WO97/31899). The dimerization of the proteins can be used to initiatetranscription of the transgene.

An alternative regulation technology uses a method of storing proteinsexpressed from the gene of interest inside the cell as an aggregate orcluster. The gene of interest is expressed as a fusion protein thatincludes a conditional aggregation domain that results in the retentionof the aggregated protein in the endoplasmic reticulum. The storedproteins are stable and inactive inside the cell. The proteins can bereleased, however, by administering a drug (e.g., small molecule ligand)that removes the conditional aggregation domain and thereby specificallybreaks apart the aggregates or clusters so that the proteins may besecreted from the cell. See Aridor et al., 2000, Science 287:816-17 andRivera et al., 2000, Science 287:826-30.

Other suitable control means or gene switches include, but are notlimited to, the systems described herein. Mifepristone (RU486) is usedas a progesterone antagonist. The binding of a modified progesteronereceptor ligand-binding domain to the progesterone antagonist activatestranscription by forming a dimer of two transcription factors that thenpass into the nucleus to bind DNA. The ligand-binding domain is modifiedto eliminate the ability of the receptor to bind to the natural ligand.The modified steroid hormone receptor system is further described inU.S. Pat. No. 5,364,791 and International Pub. Nos. WO 96/40911 and WO97/10337.

Yet another control system uses ecdysone (a fruit fly steroid hormone)that binds to and activates an ecdysone receptor (cytoplasmic receptor).The receptor then translocates to the nucleus to bind a specific DNAresponse element (promoter from ecdysone-responsive gene). The ecdysonereceptor includes a transactivation domain, DNA-binding domain, andligand-binding domain to initiate transcription. The ecdysone system isfurther described in U.S. Pat. No. 5,514,578 and International Pub. Nos.WO 97/38117, WO 96/37609, and WO 93/03162.

Another control means uses a positive tetracycline-controllabletransactivator. This system involves a mutated tet repressor proteinDNA-binding domain (mutated tet R-4 amino acid changes which resulted ina reverse tetracycline-regulated transactivator protein, i.e., it bindsto a tet operator in the presence of tetracycline) linked to apolypeptide which activates transcription. Such systems are described inU.S. Pat. Nos. 5,464,758, 5,650,298, and 5,654,168.

Additional expression control systems and nucleic acid constructs aredescribed in U.S. Pat. Nos. 5,741,679 and 5,834,186, to InnovirLaboratories Inc.

In vivo gene therapy may be accomplished by introducing the geneencoding TEM5α polypeptide into cells via local injection of a TEM5αnucleic acid molecule or by other appropriate viral or non-viraldelivery vectors. Hefti 1994, Neurobiology 25:1418-35. For example, anucleic acid molecule encoding a TEM5α polypeptide may be contained inan adeno-associated virus (AAV) vector for delivery to the targetedcells (see, e.g., International Pub. Nos. WO 95/34670 and WO 95/34670).The recombinant AAV genome typically contains AAV inverted terminalrepeats flanking a DNA sequence encoding a TEM5α polypeptide operablylinked to functional promoter and polyadenylation sequences.

Alternative suitable viral vectors include, but are not limited to,retrovirus, adenovirus, herpes simplex virus, lentivirus, hepatitisvirus, parvovirus, papovavirus, poxvirus, alphavirus, coronavirus,rhabdovirus, paramyxovirus, and papilloma virus vectors. U.S. Pat. No.5,672,344 describes an in vivo viral-mediated gene transfer systeminvolving a recombinant neurotrophic HSV-1 vector. U.S. Pat. No.5,399,346 provides examples of a process for providing a patient with atherapeutic protein by the delivery of human cells that have beentreated in vitro to insert a DNA segment encoding a therapeutic protein.Additional methods and materials for the practice of gene therapytechniques are described in U.S. Pat. Nos. 5,631,236 (involvingadenoviral vectors), 5,672,510 (involving retroviral vectors), 5,635,399(involving retroviral vectors expressing cytokines).

Nonviral delivery methods include, but are not limited to,liposome-mediated transfer, naked DNA delivery (direct injection),receptor-mediated transfer (ligand-DNA complex), electroporation,calcium phosphate precipitation, and microparticle bombardment (e.g.,gene gun). Gene therapy materials and methods may also include induciblepromoters, tissue-specific enhancer-promoters, DNA sequences designedfor site-specific integration, DNA sequences capable of providing aselective advantage over the parent cell, labels to identify transformedcells, negative selection systems and expression control systems (safetymeasures), cell-specific binding agents (for cell targeting),cell-specific internalization factors, and transcription factors toenhance expression by a vector as well as methods of vector manufacture.Such additional methods and materials for the practice of gene therapytechniques are described in U.S. Pat. Nos. 4,970,154 (involvingelectroporation techniques), 5,679,559 (describing alipoprotein-containing system for gene delivery), 5,676,954 (involvingliposome carriers), 5,593,875 (describing methods for calcium phosphatetransfection), and 4,945,050 (describing a process wherein biologicallyactive particles are propelled at cells at a speed whereby the particlespenetrate the surface of the cells and become incorporated into theinterior of the cells), and International Pub. No. WO 96/40958(involving nuclear ligands).

It is also contemplated that TEM5α gene therapy or cell therapy canfurther include the delivery of one or more additional polypeptide(s) inthe same or a different cell(s). Such cells may be separately introducedinto the patient, or the cells may be contained in a single implantabledevice, such as the encapsulating membrane described above, or the cellsmay be separately modified by means of viral vectors.

A means to increase endogenous TEM5α polypeptide expression in a cellvia gene therapy is to insert one or more enhancer elements into theTEM5α polypeptide promoter, where the enhancer elements can serve toincrease transcriptional activity of the TEM5α gene. The enhancerelements used will be selected based on the tissue in which one desiresto activate the gene—enhancer elements known to confer promoteractivation in that tissue will be selected. For example, if a geneencoding a TEM5α polypeptide is to be “turned on” in T-cells, the lckpromoter enhancer element may be used. Here, the functional portion ofthe transcriptional element to be added may be inserted into a fragmentof DNA containing the TEM5α polypeptide promoter (and optionally,inserted into a vector and/or 5′ and/or 3′ flanking sequences) usingstandard cloning techniques. This construct, known as a “homologousrecombination construct,” can then be introduced into the desired cellseither ex vivo or in vivo.

Gene therapy also can be used to decrease TEM5α polypeptide expressionby modifying the nucleotide sequence of the endogenous promoter. Suchmodification is typically accomplished via homologous recombinationmethods. For example, a DNA molecule containing all or a portion of thepromoter of the TEM5α gene selected for inactivation can be engineeredto remove and/or replace pieces of the promoter that regulatetranscription. For example, the TATA box and/or the binding site of atranscriptional activator of the promoter may be deleted using standardmolecular biology techniques; such deletion can inhibit promoteractivity thereby repressing the transcription of the corresponding TEM5αgene. The deletion of the TATA box or the transcription activatorbinding site in the promoter may be accomplished by generating a DNAconstruct comprising all or the relevant portion of the TEM5αpolypeptide promoter (from the same or a related species as the TEM5αgene to be regulated) in which one or more of the TATA box and/ortranscriptional activator binding site nucleotides are mutated viasubstitution, deletion and/or insertion of one or more nucleotides. As aresult, the TATA box and/or activator binding site has decreasedactivity or is rendered completely inactive. This construct, which alsowill typically contain at least about 500 bases of DNA that correspondto the native (endogenous) 5′ and 3′ DNA sequences adjacent to thepromoter segment that has been modified, may be introduced into theappropriate cells (either ex vivo or in vivo) either directly or via aviral vector as described herein. Typically, the integration of theconstruct into the genomic DNA of the cells will be via homologousrecombination, where the 5′ and 3′ DNA sequences in the promoterconstruct can serve to help integrate the modified promoter region viahybridization to the endogenous chromosomal DNA.

Therapeutic Uses

TEM5α nucleic acid molecules, polypeptides, and agonists and antagoniststhereof can be used to treat, diagnose, ameliorate, or prevent a numberof diseases, disorders, or conditions, including those recited herein.

TEM5α polypeptide agonists and antagonists include those molecules whichregulate TEM5α polypeptide activity and either increase or decrease atleast one activity of the mature form of the TEM5α polypeptide. Agonistsor antagonists may be co-factors, such as a protein, peptide,carbohydrate, lipid, or small molecular weight molecule, which interactwith TEM5α polypeptide and thereby regulate its activity. Potentialpolypeptide agonists or antagonists include antibodies that react witheither soluble or membrane-bound forms of TEM5α polypeptides thatcomprise part or all of the extracellular domains of the said proteins.Molecules that regulate TEM5α polypeptide expression typically includenucleic acids encoding TEM5α polypeptide that can act as anti-senseregulators of expression.

Since TEM5α polypeptide expression has been detected in the lung, TEM5αnucleic acid molecules, polypeptides, agonists and antagonists thereof(including, but not limited to, anti-TEM5α selective binding agents) maybe useful for the treatment or diagnosis of diseases involving the lung.Examples of such diseases include, but are not limited to, asthma,bronchospasm, and acute respiratory distress syndrome. Other diseasesassociated with the lung are encompassed within the scope of theinvention.

Since TEM5α polypeptide expression has been detected in the heart, TEM5αnucleic acid molecules, polypeptides, agonists and antagonists thereof(including, but not limited to, anti-TEM5α selective binding agents) maybe useful for the treatment or diagnosis of diseases involving theheart. Examples of such diseases include, but are not limited to,arrhythmias, angina, hypertension, myocardial infarction and congestiveheart failure. Other diseases associated with the heart are encompassedwithin the scope of the invention.

Since TEM5α polypeptide expression has been detected in the kidney,TEM5α nucleic acid molecules, polypeptides, agonists and antagoniststhereof (including, but not limited to, anti-TEM5α selective bindingagents) may be useful for the treatment or diagnosis of diseasesinvolving the kidney. Examples of such diseases include, but are notlimited to, polycystic kidney disease, and acute renal failure. Otherdiseases associated with the kidney are encompassed within the scope ofthe invention.

Since TEM5α polypeptide expression has been detected in the pancreas,TEM5α nucleic acid molecules, polypeptides, agonists and antagoniststhereof (including, but not limited to, anti-TEM5α selective bindingagents) may be useful for the treatment or diagnosis of diseasesinvolving the pancreas. Examples of such diseases include, but are notlimited to, diabetes, obesity, and gastro intestinal failure. Otherdiseases associated with the pancreas are encompassed within the scopeof the invention.

Expression of TEM5 has been detected in the endothelial compartment ofblood vessels in colorectal tumor (St. Croix et al., 2000, Science289:1197-202). Therefore, TEM5α polypeptides may play a role in theregulation of angiogenesis in primary and metastatic tumors.Accordingly, TEM5α nucleic acid molecules, polypeptides, agonists andantagonists thereof (including, but not limited to, anti-TEM5α selectivebinding agents) may be useful as surrogate markers for the treatment ordiagnosis of cancer diseases. Examples of such diseases include, but arenot limited to, colorectal cancer, breast cancer, lung cancer, stomachcancer, pancreatic cancer and liver cancer. Other primary and metastaticcancer diseases are encompassed within the scope of the invention.

TEM5α polypeptides may also play a role in the control of angiogenesisin inflammatory diseases. Accordingly, TEM5α nucleic acid molecules,polypeptides, agonists and antagonists thereof (including, but notlimited to, anti-TEM5α selective binding agents) may be useful for thetreatment or diagnosis of inflammatory diseases. Examples of suchdiseases include, but are not limited to, rheumatoid arthritis andinflammatory bowel disease. Other inflammatory diseases are encompassedwithin the scope of the invention.

Agonists or antagonists of TEM5α polypeptide function may be used(simultaneously or sequentially) in combination with one or morecytokines, growth factors, antibiotics, anti-inflammatories, and/orchemotherapeutic agents as is appropriate for the condition beingtreated.

Other diseases or disorders caused by or mediated by undesirable levelsof TEM5α polypeptides are encompassed within the scope of the invention.Undesirable levels include excessive levels of TEM5α polypeptides andsub-normal levels of TEM5α polypeptides.

Uses of TEM5α Nucleic Acids and Polypeptides

Nucleic acid molecules of the invention (including those that do notthemselves encode biologically active polypeptides) may be used to mapthe locations of the TEM5α gene and related genes on chromosomes.Mapping may be done by techniques known in the art, such as PCRamplification and in situ hybridization.

TEM5α nucleic acid molecules (including those that do not themselvesencode biologically active polypeptides), may be useful as hybridizationprobes in diagnostic assays to test, either qualitatively orquantitatively, for the presence of a TEM5α nucleic acid molecule inmammalian tissue or bodily fluid samples.

Other methods may also be employed where it is desirable to inhibit theactivity of one or more TEM5α polypeptides. Such inhibition may beeffected by nucleic acid molecules that are complementary to andhybridize to expression control sequences (triple helix formation) or toTEM5α mRNA. For example, antisense DNA or RNA molecules, which have asequence that is complementary to at least a portion of a TEM5α gene canbe introduced into the cell. Anti-sense probes may be designed byavailable techniques using the sequence of the TEM5α gene disclosedherein. Typically, each such antisense molecule will be complementary tothe start site (5′ end) of each selected TEM5α gene. When the antisensemolecule then hybridizes to the corresponding TEM5α mRNA, translation ofthis mRNA is prevented or reduced. Anti-sense inhibitors provideinformation relating to the decrease or absence of a TEM5α polypeptidein a cell or organism.

Alternatively, gene therapy may be employed to create adominant-negative inhibitor of one or more TEM5α polypeptides. In thissituation, the DNA encoding a mutant polypeptide of each selected TEM5αpolypeptide can be prepared and introduced into the cells of a patientusing either viral or non-viral methods as described herein. Each suchmutant is typically designed to compete with endogenous polypeptide inits biological role.

In addition, a TEM5α polypeptide, whether biologically active or not,may be used as an immunogen, that is, the polypeptide contains at leastone epitope to which antibodies may be raised. Selective binding agentsthat bind to a TEM5α polypeptide (as described herein) may be used forin vivo and in vitro diagnostic purposes, including, but not limited to,use in labeled form to detect the presence of TEM5α polypeptide in abody fluid or cell sample. The antibodies may also be used to prevent,treat, or diagnose a number of diseases and disorders, including thoserecited herein. The antibodies may bind to a TEM5α polypeptide so as todiminish or block at least one activity characteristic of a TEM5αpolypeptide, or may bind to a polypeptide to increase at least oneactivity characteristic of a TEM5α polypeptide (including by increasingthe pharmacokinetics of the TEM5α polypeptide).

TEM5α polypeptides can be used to clone TEM5α ligands using an“expression cloning” strategy. Radiolabeled (¹²⁵Iodine) TEM5αpolypeptide or “affinity/activity-tagged” TEM5α polypeptide (such as anFc fusion or an alkaline phosphatase fusion) can be used in bindingassays to identify a cell type, cell line, or tissue that expresses aTEM5α ligand. RNA isolated from such cells or tissues can then beconverted to cDNA, cloned into a mammalian expression vector, andtransfected into mammalian cells (e.g., COS or 293) to create anexpression library. Radiolabeled or tagged TEM5α polypeptide can then beused as an affinity reagent to identify and isolate the subset of cellsin this library expressing a TEM5α ligand. DNA is then isolated fromthese cells and transfected into mammalian cells to create a secondaryexpression library in which the fraction of cells expressing the TEM5αligand would be many-fold higher than in the original library. Thisenrichment process can be repeated iteratively until a singlerecombinant clone containing the TEM5α ligand is isolated. Isolation ofTEM5α ligands is useful for identifying or developing novel agonists andantagonists of the TEM5α signaling pathway. Such agonists andantagonists include TEM5α ligands, anti-TEM5α ligand antibodies, smallmolecules or antisense oligonucleotides.

The TEM5α nucleic acids of the present invention are also useful toolsfor isolating the corresponding chromosomal TEM5α polypeptide genes. Forexample, mouse chromosomal DNA containing TEM5α sequences can be used toconstruct knockout mice, thereby permitting an examination of the invivo role for TEM5α polypeptide. The human TEM5α genomic DNA can be usedto identify heritable tissue-degenerating diseases.

The following examples are intended for illustration purposes only, andshould not be construed as limiting the scope of the invention in anyway.

Example 1 Cloning of the Human TEM5α Polypeptide Genes

Generally, materials and methods as described in Sambrook et al. suprawere used to clone and analyze the genes encoding human and murine TEM5αpolypeptides.

A human TEM5α cDNA sequence was used as a probe to identify sequencescorresponding to the murine TEM5α gene in proprietary and publicexpressed sequence tag (EST) databases. The murine TEM5α sequence wasthen used as a probe to identify sequences corresponding to severalexons of the human TEM5α gene in a proprietary human genomic sequencedatabase. Human TEM5α cDNA sequences were isolated from a human kidneycDNA library panel (OriGene Technologies; Rockville, Md.) by PCR usingamplimers derived from the predicted exon sequences of the human TEM5αgene (5′-G-T-G-G-T-G-G-T-T-C-A-T-C-A-G-G-A-T-C-C-3′; SEQ ID NO: 8 and5′-C-T-T-C-A-C-T-A-T-T-C-C-A-C-C-C-T-T-G-C-3′; SEQ ID NO: 9). Afteridentifying three positive cDNA pools using this first amplimer pair,the full-length coding sequence for the human TEM5α gene was isolatedusing four amplimer pairs (pair #1:5′-G-G-G-C-G-G-T-A-G-G-C-G-T-G-T-A-C-G-G-T-G-G-3′; SEQ ID NO: 10 and5′-G-C-A-T-G-T-C-A-A-C-A-G-C-T-C-C-T-G-C-3′; SEQ ID NO: 11; pair #2:5′-C-C-A-G-A-C-T-G-A-G-T-A-T-C-T-T-T-T-G-3′; SEQ ID NO: 12 and5′-G-C-A-A-T-G-C-G-C-T-G-A-A-G-A-C-A-C-T-G-3′; SEQ ID NO: 13; pair#3:5′-A-G-G-T-G-A-C-G-T-G-A-T-G-G-T-T-G-A-C-3′; SEQ ID NO: 14 and5′G-T-G-G-T-G-G-T-T-C-A-T-C-A-G-G-A-T-C-C-3′; SEQ ID NO: 15; pair #4:5′G-G-G-A-G-G-G-G-T-C-A-C-A-G-G-G-A-T-G-3′, SEQ ID NO: 16 and5′-C-T-T-C-A-C-T-A-T-T-C-C-A-C-C-C-T-T-G-C-3′; SEQ ID NO: 17). The PCRproducts generated in this second amplification reaction were subclonedinto the pCR 2.1 vector (Invitrogen) and positive clones were sequenced.A consensus sequence for the human TEM5α gene was derived from thesequences obtained for at least three clones.

Sequence analysis of the full-length cDNA for human TEM5α polypeptideindicated that the gene comprises a 3963 bp open reading frame encodinga protein of 1321 amino acids. FIGS. 1A-1G show the nucleotide sequenceof the human TEM5α gene and the deduced amino acid sequence of the humanTEM5α polypeptide.

One of the three positive pools from the initial library screening wasfound to comprise a TEM5α nucleic acid sequence containing a 14 basepair insertion between bases 1830 and 1831 of the nucleotide sequenceshown in FIGS. 1A-1G. This insertion results in a prematuretranslational stop, forming a short (559 amino acids), soluble form ofTEM5α (sTEM5α). FIGS. 2A-2D show the nucleotide sequence and deducedamino acid sequence of sTEM5α polypeptide.

The TEM5α and sTEM5α nucleic acid sequences encode polypeptides that arerelated to tumor endothelial marker 5 (TEM5) (St. Croix et al., 2000,Science 289:1197-202). FIGS. 3A-3B illustrate an amino acid sequencealignment of human TEM5α polypeptide (huTEM5α; SEQ ID NO: 4) and humanTEM5. The human TEM5α gene shares a 63.5% similarity with the human TEM5gene and human TEM5α polypeptide shares a 60% similarity with human TEM5polypeptide. The structure of both human and mouse TEM5α polypeptideparallels that of TEM5α in that both polypeptides contain a predictedsignal peptide sequence in the N-terminus and seven transmembranedomains near the C-terminus, suggesting that TEM5α is a membrane-boundprotein. The sTEM5α polypeptide comprises a predicted signal peptide andan extracellular domain, and lacks the seven transmembrane domains.

A BLAST analysis of the amino acid sequences for the human TEM5αpolypeptide and the soluble form of the human TEM5α polypeptideperformed against the Conserved Domain Database (a collection offunctional and structural domains derived primarily from the Smart andPfam databases) indicated that these proteins possess a number ofconserved protein domains. Specifically, both the full-length andsoluble forms possess a leucine-rich repeat C-terminal (LRRCT) domain(indicated as domains A and B in FIGS. 4A and 4B), an immunoglobulin(Ig) domain (indicated as domains C and D in FIGS. 4A and 4B), and ahormone receptor (HRM) domain (indictaed as domain E in FIGS. 4A and 4Band domain K in FIG. 4B). The BLAST analysis also indicated that thehuman TEM5α polypeptide also possesses a G-protein coupled receptorprotelytic site (GPS) domain (indicated as domains F and G in FIG. 4A)and a 7 transmembrane receptor (7tm_(—)2) domain (indicated as domain Hin FIG. 4A). The BLAST analysis further indicated that the soluble formof the human TEM5α polypeptide possesses a leucine-rich repeat (LRR)domain (panels I and J in FIG. 4B).

The sequence of the human TEM5α gene was used to search both the CELERAhuman genomic and GenBank databases. The human TEM5α gene was found tospan about 132 kb and consist of 19 exons and 18 introns. Exon 1 of thehuman TEM5α gene was located in GenBank Accession No. AC093814, andexons 2 through 19 were identified in the CELERA human genomic database.Exon/intron junctions were predicted using Fichant's rule (Fichant,1992, Hum. Mol. Genet. 1:259-67). The location and the numbers ofexon/intron junctions for TEM5α are similar to those of TEM5, suggestingthat the two genes derive from a common ancestor.

The human TEM5α gene was located in a large contig sequence in theCELERA human genomic database, oriented in an anti-sense directiontoward the telomere of the p arm of chromosome 4. This contig sequencealso contains the cytosolic β-glucosidase (CBG; GenBANK Accession No.AF323990), peroxisome proliferator-activated receptor γ (PPARGC1,GenBANK Accession No. NM_(—)013261), and SLIT2 (GenBANK Accession No. NM004787) genes. The human CBG gene is about 158 kb proximal to the humanTEM5α gene, and the human PPARGC1 gene is about 1250 kb proximal to thehuman TEM5α gene. In the distal region, the human SLIT2 gene is about1890 kb away from the human TEM5α gene. The CBG, PPARGC1, and SLIT2genes have been mapped to the human chromosome 4p15 region, suggestingthat the human TEM5α gene will be located in this region as well.

Example 2 TEM5α mRNA Expression

The expression of human TEM5α was analyzed by PCR using amplimersderived from the predicted exon sequence as described in Example 1 (5′G-T-G-G-T-G-G-T-T-C-A-T-C-A-G-G-A-T-C-C-3′; SEQ ID NO: 8 and5′-C-T-T-C-A-C-T-A-T-T-C-C-A-C-C-C-T-T-G-C-3′; SEQ ID NO: 9). Theexpected PCR product (112 bp) was detected in heart, lung, kidney,pancreas, placenta, brain, skeletal muscle, ovary, liver, prostate, andtestis. The expected PCR product was not detected in spleen, thymus, orleukocytes. TEM5 has been shown to be elevated in the endothelialcompartment of blood vessels in colorectal tumors. TEM5 (as well asother members of the TEM family) expression has also been shown insarcomas and in primary cancers of the lung, breast, brain, andpancreas. In addition, TEM expression has been shown in metastaticendothelial tissues.

The expression of TEM5α mRNA is examined by Northern blot analysis.Multiple human tissue northern blots (Clontech) are probed with asuitable restriction fragment isolated from a human TEM5α polypeptidecDNA clone. The probe is labeled with ³²P-dCTP using standardtechniques.

Northern blots are prehybridized for 2 hours at 42° C. in hybridizationsolution (5×SSC, 50% deionized formamide, 5×Denhardt's solution, 0.5%SDS, and 100 mg/ml denatured salmon sperm DNA) and then hybridized at42° C. overnight in fresh hybridization solution containing 5 ng/ml ofthe labeled probe. Following hybridization, the filters are washed twicefor 10 minutes at room temperature in 2×SSC and 0.1% SDS, and then twicefor 30 minutes at 65° C. in 0.1×SSC and 0.1% SDS. The blots are thenexposed to autoradiography.

The expression of TEM5α mRNA is localized by in situ hybridization. Apanel of normal embryonic and adult mouse tissues is fixed in 4%paraformaldehyde, embedded in paraffin, and sectioned at 5 μm. Sectionedtissues are permeabilized in 0.2 M HCl, digested with Proteinase K, andacetylated with triethanolamine and acetic anhydride. Sections areprehybridized for 1 hour at 60° C. in hybridization solution (300 mMNaCl, 20 mM Tris-HCl, pH 8.0, 5 mM EDTA, 1×Denhardt's solution, 0.2%SDS, 10 mM DTT, 0.25 mg/ml tRNA, 25 μg/ml polyA, 25 μg/ml polyC and 50%formamide) and then hybridized overnight at 60° C. in the same solutioncontaining 10% dextran and 2×10⁴ cpm/μl of a ³³P-labeled antisenseriboprobe complementary to the human TEM5α gene. The riboprobe isobtained by in vitro transcription of a clone containing human TEM5αcDNA sequences using standard techniques.

Following hybridization, sections are rinsed in hybridization solution,treated with RNaseA to digest unhybridized probe, and then washed in0.1×SSC at 55° C. for 30 minutes. Sections are then immersed in NTB-2emulsion (Kodak, Rochester, N.Y.), exposed for 3 weeks at 4° C.,developed, and counterstained with hematoxylin and eosin. Tissuemorphology and hybridization signal are simultaneously analyzed bydarkfield and standard illumination for brain (one sagittal and twocoronal sections), gastrointestinal tract (esophagus, stomach, duodenum,jejunum, ileum, proximal colon, and distal colon), pituitary, liver,lung, heart, spleen, thymus, lymph nodes, kidney, adrenal, bladder,pancreas, salivary gland, male and female reproductive organs (ovary,oviduct, and uterus in the female; and testis, epididymus, prostate,seminal vesicle, and vas deferens in the male), BAT and WAT(subcutaneous, peri-renal), bone (femur), skin, breast, and skeletalmuscle.

Example 3 Production of TEM5α Polypeptides A. Expression of TEM5αPolypeptides in Bacteria

PCR is used to amplify template DNA sequences encoding a TEM5αpolypeptide using primers corresponding to the 5′ and 3′ ends of thesequence. The amplified DNA products may be modified to containrestriction enzyme sites to allow for insertion into expression vectors.PCR products are gel purified and inserted into expression vectors usingstandard recombinant DNA methodology. An exemplary vector, such aspAMG21 (ATCC no. 98113) containing the lux promoter and a gene encodingkanamycin resistance is digested with Bam HI and Nde I for directionalcloning of inserted DNA. The ligated mixture is transformed into an E.coli host strain by electroporation and transformants are selected forkanamycin resistance. Plasmid DNA from selected colonies is isolated andsubjected to DNA sequencing to confirm the presence of the insert.

Transformed host cells are incubated in 2×YT medium containing 30 μg/mLkanamycin at 30° C. prior to induction. Gene expression is induced bythe addition of N-(3-oxohexanoyl)-dl-homoserine lactone to a finalconcentration of 30 ng/mL followed by incubation at either 30° C. or 37°C. for six hours. The expression of TEM5α polypeptide is evaluated bycentrifugation of the culture, resuspension and lysis of the bacterialpellets, and analysis of host cell proteins by SDS-polyacrylamide gelelectrophoresis.

Inclusion bodies containing TEM5α polypeptide are purified as follows.Bacterial cells are pelleted by centrifugation and resuspended in water.The cell suspension is lysed by sonication and pelleted bycentrifugation at 195,000×g for 5 to 10 minutes. The supernatant isdiscarded, and the pellet is washed and transferred to a homogenizer.The pellet is homogenized in 5 mL of a Percoll solution (75% liquidPercoll and 0.15 M NaCl) until uniformly suspended and then diluted andcentrifuged at 21,600×g for 30 minutes. Gradient fractions containingthe inclusion bodies are recovered and pooled. The isolated inclusionbodies are analyzed by SDS-PAGE.

A single band on an SDS polyacrylamide gel corresponding to E.coli-produced TEM5α polypeptide is excised from the gel, and theN-terminal amino acid sequence is determined essentially as described byMatsudaira et al., 1987, J. Biol. Chem. 262:10-35.

B. Expression of TEM5α Polypeptide in Mammalian Cells

PCR is used to amplify template DNA sequences encoding a TEM5αpolypeptide using primers corresponding to the 5′ and 3′ ends of thesequence. The amplified DNA products may be modified to containrestriction enzyme sites to allow for insertion into expression vectors.PCR products are gel purified and inserted into expression vectors usingstandard recombinant DNA methodology. An exemplary expression vector,pCEP4 (Invitrogen), that contains an Epstein-Barr virus origin ofreplication, may be used for the expression of TEM5α polypeptides in293-EBNA-1 cells. Amplified and gel purified PCR products are ligatedinto pCEP4 vector and introduced into 293-EBNA cells by lipofection. Thetransfected cells are selected in 100 μg/mL hygromycin and the resultingdrug-resistant cultures are grown to confluence. The cells are thencultured in serum-free media for 72 hours. The conditioned media isremoved and TEM5α polypeptide expression is analyzed by SDS-PAGE.

TEM5α polypeptide expression may be detected by silver staining.Alternatively, TEM5α polypeptide is produced as a fusion protein with anepitope tag, such as an IgG constant domain or a FLAG epitope, which maybe detected by Western blot analysis using antibodies to the peptidetag.

TEM5α polypeptides may be excised from an SDS-polyacrylamide gel, orTEM5α fusion proteins are purified by affinity chromatography to theepitope tag, and subjected to N-terminal amino acid sequence analysis asdescribed herein.

C. Expression and Purification of TEM5α Polypeptide in Mammalian Cells

TEM5α polypeptide expression constructs are introduced into 293 EBNA orCHO cells using either a lipofection or calcium phosphate protocol.

To conduct functional studies on the TEM5α polypeptides that areproduced, large quantities of conditioned media are generated from apool of hygromycin selected 293 EBNA clones. The cells are cultured in500 cm Nunc Triple Flasks to 80% confluence before switching to serumfree media a week prior to harvesting the media. Conditioned media isharvested and frozen at

−20° C. until purification.

Conditioned media is purified by affinity chromatography as describedbelow. The media is thawed and then passed through a 0.2 μm filter. AProtein G column is equilibrated with PBS at pH 7.0, and then loadedwith the filtered media. The column is washed with PBS until theabsorbance at A₂₈₀ reaches a baseline. TEM5α polypeptide is eluted fromthe column with 0.1 M Glycine-HCl at pH 2.7 and immediately neutralizedwith 1 M Tris-HCl at pH 8.5. Fractions containing TEM5α polypeptide arepooled, dialyzed in PBS, and stored at −70° C.

For Factor Xa cleavage of the human TEM5α polypeptide-Fc fusionpolypeptide, affinity chromatography-purified protein is dialyzed in 50mM Tris-HCl, 100 mM NaCl, 2 mM CaCl₂ at pH 8.0. The restriction proteaseFactor Xa is added to the dialyzed protein at 1/100 (w/w) and the sampledigested overnight at room temperature.

Example 4 Production of Anti-TEM5α Polypeptide Antibodies

Antibodies to TEM5α polypeptides may be obtained by immunization withpurified protein or with TEM5α peptides produced by biological orchemical synthesis. Suitable procedures for generating antibodiesinclude those described in Hudson and Bay, Practical Immunology (2nded., Blackwell Scientific Publications).

In one procedure for the production of antibodies, animals (typicallymice or rabbits) are injected with a TEM5α antigen (such as a TEM5αpolypeptide), and those with sufficient serum titer levels as determinedby ELISA are selected for hybridoma production. Spleens of immunizedanimals are collected and prepared as single cell suspensions from whichsplenocytes are recovered. The splenocytes are fused to mouse myelomacells (such as Sp2/0-Ag14 cells), are first incubated in DMEM with 200U/mL penicillin, 200 μg/mL streptomycin sulfate, and 4 mM glutamine, andare then incubated in HAT selection medium (hypoxanthine, aminopterin,and thymidine). After selection, the tissue culture supernatants aretaken from each fusion well and tested for anti-TEM5α antibodyproduction by ELISA.

Alternative procedures for obtaining anti-TEM5α antibodies may also beemployed, such as the immunization of transgenic mice harboring human Igloci for production of human antibodies, and the screening of syntheticantibody libraries, such as those generated by mutagenesis of anantibody variable domain.

Example 5 Expression of TEM5α Polypeptide in Transgenic Mice

To assess the biological activity of TEM5α polypeptide, a constructencoding a TEM5α polypeptide/Fc fusion protein under the control of aliver specific ApoE promoter is prepared. The delivery of this constructis expected to cause pathological changes that are informative as to thefunction of TEM5α polypeptide. Similarly, a construct containing thefull-length TEM5α polypeptide under the control of the beta actinpromoter is prepared. The delivery of this construct is expected toresult in ubiquitous expression.

To generate these constructs, PCR is used to amplify template DNAsequences encoding a TEM5α polypeptide using primers that correspond tothe 5′ and 3′ ends of the desired sequence and which incorporaterestriction enzyme sites to permit insertion of the amplified productinto an expression vector. Following amplification, PCR products are gelpurified, digested with the appropriate restriction enzymes, and ligatedinto an expression vector using standard recombinant DNA techniques. Forexample, amplified TEM5α polypeptide sequences can be cloned into anexpression vector under the control of the human β-actin promoter asdescribed by Graham et al., 1997, Nature Genetics, 17:272-74 and Ray etal., 1991, Genes Dev. 5:2265-73.

Following ligation, reaction mixtures are used to transform an E. colihost strain by electroporation and transformants are selected for drugresistance. Plasmid DNA from selected colonies is isolated and subjectedto DNA sequencing to confirm the presence of an appropriate insert andabsence of mutation. The TEM5α polypeptide expression vector is purifiedthrough two rounds of CsCl density gradient centrifugation, cleaved witha suitable restriction enzyme, and the linearized fragment containingthe TEM5α polypeptide transgene is purified by gel electrophoresis. Thepurified fragment is resuspended in 5 mM Tris, pH 7.4, and 0.2 mM EDTAat a concentration of 2 mg/mL.

Single-cell embryos from BDF1×BDF1 bred mice are injected as described(International Pub. No. WO 97/23614). Embryos are cultured overnight ina CO₂ incubator and 15-20 two-cell embryos are transferred to theoviducts of a pseudopregnant CD1 female mice. Offspring obtained fromthe implantation of microinjected embryos are screened by PCRamplification of the integrated transgene in genomic DNA samples asfollows. Ear pieces are digested in 20 mL ear buffer (20 mM Tris, pH8.0, 10 mM EDTA, 0.5% SDS, and 500 mg/mL proteinase K) at 55° C.overnight. The sample is then diluted with 200 mL of TE, and 2 mL of theear sample is used in a PCR reaction using appropriate primers.

At 8 weeks of age, transgenic founder animals and control animals aresacrificed for necropsy and pathological analysis. Portions of spleenare removed and total cellular RNA isolated from the spleens using theTotal RNA Extraction Kit (Qiagen) and transgene expression determined byRT-PCR. RNA recovered from spleens is converted to cDNA using theSuperScript™ Preamplification System (Gibco-BRL) as follows. A suitableprimer, located in the expression vector sequence and 3′ to the TEM5αpolypeptide transgene, is used to prime cDNA synthesis from thetransgene transcripts. Ten mg of total spleen RNA from transgenicfounders and controls is incubated with 1 mM of primer for 10 minutes at70° C. and placed on ice. The reaction is then supplemented with 10 mMTris-HCl, pH 8.3, 50 mM KCl, 2.5 mM MgCl₂, 10 mM of each dNTP, 0.1 mMDTT, and 200 U of SuperScript II reverse transcriptase. Followingincubation for 50 minutes at 42° C., the reaction is stopped by heatingfor 15 minutes at 72° C. and digested with 2U of RNase H for 20 minutesat 37° C. Samples are then amplified by PCR using primers specific forTEM5α polypeptide.

Example 6 Biological Activity of TEM5α Polypeptide in Transgenic Mice

Prior to euthanasia, transgenic animals are weighed, anesthetized byisofluorane and blood drawn by cardiac puncture. The samples aresubjected to hematology and serum chemistry analysis. Radiography isperformed after terminal exsanguination. Upon gross dissection, majorvisceral organs are subject to weight analysis.

Following gross dissection, tissues (i.e., liver, spleen, pancreas,stomach, the entire gastrointestinal tract, kidney, reproductive organs,skin and mammary glands, bone, brain, heart, lung, thymus, trachea,esophagus, thyroid, adrenals, urinary bladder, lymph nodes and skeletalmuscle) are removed and fixed in 10% buffered Zn-Formalin forhistological examination. After fixation, the tissues are processed intoparaffin blocks, and 3 mm sections are obtained. All sections arestained with hematoxylin and exosin, and are then subjected tohistological analysis.

The spleen, lymph node, and Peyer's patches of both the transgenic andthe control mice are subjected to immunohistology analysis with B-celland T-cell specific antibodies as follows. The formalin fixed paraffinembedded sections are deparaffinized and hydrated in deionized water.The sections are quenched with 3% hydrogen peroxide, blocked withProtein Block (Lipshaw, Pittsburgh, Pa.), and incubated in ratmonoclonal anti-mouse B220 and CD3 (Harlan, Indianapolis, Ind.).Antibody binding is detected by biotinylated rabbit anti-ratimmunoglobulins and peroxidase conjugated streptavidin (BioGenex, SanRamon, Calif.) with DAB as a chromagen (BioTek, Santa Barbara, Calif.).Sections are counterstained with hematoxylin.

After necropsy, MLN and sections of spleen and thymus from transgenicanimals and control littermates are removed. Single cell suspensions areprepared by gently grinding the tissues with the flat end of a syringeagainst the bottom of a 100 mm nylon cell strainer (Becton Dickinson,Franklin Lakes, N.J.). Cells are washed twice, counted, andapproximately 1×10⁶ cells from each tissue are then incubated for 10minutes with 0.5 μg CD16/32(FcγIII/II) Fc block in a 20 μL volume.Samples are then stained for 30 minutes at 2-8° C. in a 100 μL volume ofPBS (lacking Ca⁺ and Mg⁺), 0.1% bovine serum albumin, and 0.01% sodiumazide with 0.5 μg antibody of FITC or PE-conjugated monoclonalantibodies against CD90.2 (Thy-1.2), CD45R (B220), CD11b (Mac-1), Gr-1,CD4, or CD8 (PharMingen, San Diego, Calif.). Following antibody binding,the cells are washed and then analyzed by flow cytometry on a FACScan(Becton Dickinson).

While the present invention has been described in terms of the preferredembodiments, it is understood that variations and modifications willoccur to those skilled in the art. Therefore, it is intended that theappended claims cover all such equivalent variations that come withinthe scope of the invention as claimed.

1. A method of determining an amount of TEM5α polypeptide present in asample comprising: (a) contacting the sample with a detectably labeledantibody that specifically binds to SEQ ID NO:2 or 4; and (b)determining the amount of antibody bound to the sample; and (c)correlating the amount of antibody bound to the sample with the amountof TEM5α present in the sample.
 2. The method of claim 1, wherein themethod comprises a component of a competitive binding assay.
 3. Themethod of claim 1, wherein the method comprises a component of a directsandwich assay.
 4. The method of claim 1, wherein the assay comprises acomponent of an indirect sandwich assay.
 5. The method of claim 1,wherein the assay comprises a component of an immunoprecipitation assay.6. The method of claim 1, wherein the detectable label comprises afluorescent moiety.
 7. The method of claim 1, wherein the detectablelabel comprises a radiolabel.